Visual Census Research Articles

Ictiofauna y calidad del agua en el sitio ecoturístico “El Remate” Campeche, Mexico: muestreo prospectivo antes del Tren Maya

A prospective punctual sampling was carried out during the rainy season where the quality of the water (nutrients such as: nitrites, sulfates, phosphates and ammonium) and the fish community (ichthyofauna) were measured by means of UVC methodology (underwater visual census), in the ecotourism site “El Remate” which is located in the municipality of Calkiní, Campeche, where an increase in tourism is expected from the “Mayan Train” megaproject. Water quality tests did not reflect a significant anthropic impact on the water body and the ichthyofauna presented ecological characteristics similar to those reported by Torres-Castro et al. (2009), although the number of reported species decreased. The results of this study are proposed as ecological references to continue monitoring this ecosystem and thus address the uncertainty about the impact of the increase in tourist influx on ecosystems of this type. Keywords: UVC methodology, water quality, anthropic impact, Campeche.

Chatting behind the reef: Fish bioacoustic diversity of tropical back-reefs in Fiji, South Pacific

Back-reef habitats are important and fragile transition zones acting as nurseries for many coral reef fishes. In this framework, Passive Acoustic Monitoring (PAM) can be an important tool to evaluate the diversity and dynamics of sonic fish community. Here, we investigated the diversity, spatial and diel dynamics of fish sounds in back-reef habitats at Makogai Island in Fiji, South Pacific. Synchronized underwater recorders were deployed in 4 bays collecting data for about 4 days. The abundance of 12 different sub-categories of fish sounds were quantified. Signals were acoustically characterized and the level of discrimination between the sub-categories was evaluated by Discrimination Function Analysis. Generalized Additive Models showed that the abundance of signals was related to the bay and the hour. Moreover, the Shannon Diversity and Equitability Indices were calculated using acoustic and visual census data to describe fish biodiversity of each bay. The two bays with greater biodiversity based on visual census also showed a greater acoustic diversity at dawn and night. Our results highlight the importance of PAM to reveal the diversity of fish community in back-reef habitats, providing a baseline to understand future changes in these crucial environments.

Baseline for marine cave monitoring strategies in the Alboran Sea using modified Cave Ecosystem-Based Quality Index (CavEBQI)

Marine caves constitute vulnerable habitats with unique and diverse biocoenoses. Monitoring these habitats is still challenging, which hinders the ability to evaluate global and local pressures that threatens their ecological value. In this study, ecological quality is estimated in twenty-one marine caves distributed along the northern and southern coasts of the Alboran Sea, a highly understudied area regarding marine caves. For that purpose, adjustments on the original Cave Ecosystem Based Quality Index (CavEBQI) are suggested in order to efficiently estimate the ecological quality of marine caves. Several methodological aspects regarding the assessment of biotic coverage, the visual census of motile fauna and the plasticity of the index usability were evaluated. Ecological quality of marine caves was in average “good” although it ranged between “poor”, “moderate” and “good” depending on the features of each cave. This study emphasizes the importance of adapting biotic indicators to biogeographical differences and technological advancements.

Deep Dive Into Noninvasive Biometrics: A Pilot Journey Using Stereo-Video in a Public Aquarium.

Accurate collection of biometric data is important for understanding the biology and conservation of marine organisms, including elasmobranch and teleost fish, both in nature and controlled environments where monitoring marine specimens' health is mandatory. Traditional methods involving specimen capture and handling are invasive, stressful, and disruptive. Some techniques like underwater visual census or laser photogrammetry have been used for noninvasive data collection, but they have limitations and biases. The application of stereo-video photogrammetry through the use of diver-operated stereo-video systems (stereo-DOV) is a noninvasive method that overcomes these challenges, providing highly accurate measurements. It has become popular for species monitoring, studying anthropogenic impacts, and assessing length distributions. However, this technique is still uncommon and barely reported in aquarium settings. This study describes an innovative pilot study targeting multiple species carried out in a Public Aquarium, using a low-cost house-made device. The results revealed that measuring more than 100 individuals in approximately 1 day's work is possible. Total and fork lengths were estimated using specific software for 31 teleost and 16 elasmobranch species and compared with real measurements for the available species. Despite technical limitations that must be reviewed for application in future studies that resulted in high root mean square (RMS) values (> 20 mm), differences between methodological approaches revealed a minimal discrepancy (1.37%-5% in large sharks and rays and 1.8%-5.5% in teleost fish). This technique has time and cost requirements, but might represent a major advance in husbandry and in the contribution to conservation that ex situ studies can provide.

Pollinator diversity of the food-deceptive orchids in southern Italy.

The orchid family is renowned for its enormous diversity in pollination biology. Many orchid species use deception to attract pollinators, and the main strategy in terrestrial orchids is food deception. Food-deceptive orchids usually show a low number of pollinator visitations, making field observations of pollinators difficult. In this study visual census, pollinator capture and molecular analysis of pollinaria found on caught insects allowed us to obtain information on species composition of orchid pollinators. A total of 321 insects were caught; most specimens were hymenopterans (Apis mellifera, Bombus ruderatus and Eucera rufa) and coleopterans (Tropinota hirta and T. squalida). The identity of species to which pollinaria found on the insect's body belonged was confirmed by molecular analysis. Moreover, some individuals of Billaea lata (Tachinidae, Diptera) were captured and photographed with the pollinaria on their head. Two new and important results emerged clearly in this work: a dipteran, Billaea lata, pollinator of Anacamptis pyramidalis, and two beetles in the genus Tropinota are pollinators of Orchis italica. Our results confirm that generalized food-deceptive orchids of the genera Orchis and Anacamptis show weak pollinator specificity.

Multidecadal underwater surveys reveal declines in marine turtles

AbstractMarine turtles are a group of imperiled marine megafauna particularly vulnerable to anthropogenic stressors. Most long‐term studies of marine turtles are based on nesting surveys which focus on numbers of eggs, hatchlings, and nesting females. However, we know less about long‐term abundance trends of immature and adult turtles in the marine environment. To address this data gap, we examined records from 35,000 underwater visual census (UVC) dives (1993–2019) and short‐term in‐water turtle survey data (2009–2014) at Cocos Island, Costa Rica. During UVCs, trained divemasters from UnderSea Hunter recorded observations of two species of marine turtles—green Chelonia mydas and hawksbill Eretmochelys imbricata. Our short‐term in‐water surveys revealed that most turtles at Cocos are greens, but both immature and mature greens occur at Cocos. We analyzed long‐term UVC data using a hierarchical modeling approach and we modeled a 26% decrease in the relative abundance of turtles observed on dives each year. Our model also revealed potential interactions between tiger sharks and turtles, finding that for each additional tiger shark present during a dive, the predicted relative abundance of turtles decreased by 43%. Lastly, our model suggested the influence of environmental variation on marine turtle relative abundance; a 1°C increase in sea surface temperature (SST) decreased the predicted relative abundance of turtles by 7%. Our results suggest that marine turtles are sensitive to long‐term environmental and oceanographic changes, and potentially avoid certain areas to reduce exposure to tiger sharks. Given our study area is already protected, there needs to be more focus on protecting adult turtles during their movements across the Eastern Tropical Pacific. Our work also highlights the importance of long‐term underwater surveys to monitor adult turtles.

New evidence of alternative migration patterns for two Mediterranean potamodromous species

Iberian barbel (Luciobarbus bocagei Steindachner, 1864) and Iberian nase (Pseudochondrostoma polylepis Steindachner, 1864) are two Mediterranean potamodromous fish species known to perform annual upstream migrations to reach spring spawning grounds. In the Mondego River basin, at the Coimbra dam, migratory movement patterns and individual size structure were assessed through a video recording monitoring system installed on an upstream section of a vertical-slot fish pass. Visual census for these target species during two consecutive annual cycles (2013–2014) revealed alternative migratory patterns, with the first peak of upstream movements in autumn, for both barbel (October–November) and nase (November–December). Circadian movements of both species showed a diurnal preference, contrary to what is usually described for these species. Size structure analysis for individuals of both species showed significant intra-annual differences in the size of migrating fish. Boosted regression trees models applied to the 2013–2014 visual count data identified flow and temperature as the most influential environmental predictors, triggering both species’ movements in each direction in the study years. These results provide novel information on the timing of the migratory movements of these potamodromous fish, which can be used to adapt current management and conservation measures to the specificities of their migratory behaviour.

Spatial and Temporal Dynamics of the Canine Population and Contamination by Canine Feces on an Urban Beach

Objective: The objective of this study was to analyze the spatio-temporal distribution of dogs and feces using the visual census method. The research aimed to quantify the presence of dogs and the number of feces observed in these environments. Method: The visual census was conducted every fifteen days over the course of one year along the Mar Grosso beach shoreline, which was divided into areas and sectors. The data were subsequently tabulated, and statistical analysis was performed using the non-parametric Kruskal-Wallis test. Research Results and Discussions: The highest number of feces and stray dogs were found in the urban sector during the summer. Regarding the areas observed and feces, the area with the highest number of feces was A3 in the urban sector during the summer. As for the number of stray, domiciled, and off-leash dogs, they were more frequently observed in the summer, with stray dogs predominantly in A2 (beach sector), and domiciled and off-leash dogs in A3 and A2, respectively, in the urban sector. Research Implications: The results identify hotspots of feces and dogs along the study area, providing valuable information that can assist in decision-making and the implementation of public policies aimed at controlling animals on beaches and protecting the environment, thereby reducing the risk of disease transmission to the population frequenting these locations. Originality/Value: This study contributes to evidence-based policy implementation to promote environmental health, public health, and animal welfare in coastal areas.

Community Structure of Fishes the Association with Seagrasses at Bama Beach, Baluran National Park, Situbondo, East Java

Seagrass bed has an important role for biota in waters. The existence of fish in seagrass is influenced by other ecosystems close to seagrass, such as mangroves and coral reefs. This study focuses on fish associated with seagrass in Bama Beach. The data include seagrass coverage and the number of fish for the Diversity, Uniformity, and Dominance. The study was carried out on March 15 to 20, 2018 using the Underwater Visual Census. Results show that seagrass cover was highest in seagrass stations near mangroves (62,66%), while at stations near coral reefs was 37,66. The composition of fish associated with seagrass near mangroves was 361 individuals, while near reefs was 1.454 individuals. The values of diversity, uniformity, and dominance of fish associated with seagrass near mangroves are 2,62; 0,88; and 0,09 respectively while those associated with coral reefs have values of 2,93; 0,85; and 0,06. Family Aulostomidae was dominant in the morning at the station near mangroves, and in the afternoon was dominated by Apogonidae. At the station near coral reefs, the Family Pomacentridae was dominant both in the morning and afternoon. The seagrass conditions in this study are in the healthy category with quite diverse fishes. The level of fish diversity in seagrass was influenced by habitats associated with seagrasses than seagrass cover levels. The condition of Bama Beach as a conservation area is quite good, but the activity of tourists around the coastline must be monitored to maintain the environment.

Monitoring macroplastics in aquatic and terrestrial ecosystems: Expert survey reveals visual and drone-based census as most effective techniques

Anthropogenic litter, such as plastic, is investigated by the global scientific community from various fields employing diverse techniques. The goal is to assess and finally mitigate the pollutants' impacts on the natural environment. Plastic litter can accumulate in different matrices of aquatic and terrestrial ecosystems, impacting both biota and ecosystem functioning. Detection and quantification of macroplastics, and other litter, can be realized by jointly using visual census and remote sensing techniques. The primary objective of this research was to identify the most effective approach for monitoring macroplastic litter in riverine and marine environments through a comprehensive survey based on the experiences of the scientific community. Researchers involved in plastic pollution evaluated four litter occurrence and flux investigation methods (visual census, drone-based surveys, satellite imagery, and GPS/GNSS trackers) through a questionnaire. Traditional visual census and drone deployment were deemed as the most popular approaches among the 46 surveyed researchers, while satellite imagery and GPS/GNSS trackers received lower scores due to limited field validation and short performance ranges, respectively. On a scale from 0 to 5, visual census and drone-based surveys obtained 3.5 and 2.0, respectively, whereas satellite imagery and alternative solutions received scores lower than 1.2. Visual and drone censuses were used in high, medium and low-income countries, while satellite census and GPS/GNSS trackers were mostly used in high-income countries. This work provides an overview of the advantages and drawbacks of litter investigation techniques, contributing i) to the global harmonization of macroplastic litter monitoring and ii) providing a starting point for researchers and water managers approaching this topic. This work supports the selection and design of reliable and cost-effective monitoring approaches to mitigate the ambiguity in macroplastic data collection, contributing to the global harmonization of macroplastic litter monitoring protocols.

When the Light Goes Out: Distribution and Sleeping Habitat Use of Parrotfishes at Night

Understanding the diurnal and nocturnal activity of organisms is a key topic in behavioral ecology, with implications for population structure and management strategies. In reef systems, parrotfishes play crucial roles as nominal herbivores, but overfishing has led to population collapses with detrimental effects on reef functions. Parrotfish are good models to study diel rhythms, as they are often easily observed while sleeping at night. We assessed the distribution, sleeping substrate selectivity and sleeping areas of parrotfishes during the night in a subtropical rocky reef of the Southwestern Atlantic. We performed replicated visual censuses (50 × 2 m) at different depths to estimate parrotfish abundance, while quantifying the structural complexity of sleeping sites. Among the seven recorded parrotfish species, we focused on the four most abundant to determine their sleeping habitat selectivity. Active telemetry was used for the two most abundant species to define their sleeping site areas and sleeping hotspots. All four species exhibited a preference for sediment as a sleeping substrate, while avoiding zoanthids. Species distribution was influenced by depth, with Scarus zelindae predominantly sleeping in high-complexity substrate at intermediate depths and Sparisoma tuiupiranga sleeping in the rock–sand interface at deeper depths. Tagged Sparisoma axillare and Sparisoma frondosum exhibited similar sleeping areas in terms of size and geographical locations; showing high site fidelity, they returned to the same sleeping sites over consecutive nights. These results represent the first assessment of parrotfish distribution and habitat use at night in the Atlantic. This information is crucial for guiding management actions, particularly in the planning of no-take zones for fishing control and population recovery.

High diversity and abundance of fish and coral in an artificial breakwater in Colombo, Sri Lanka

The diversity of reef fishes and the diversity and abundance of corals in artificial breakwaters were studied between June and August 2023 in Port City, Colombo in the Western Province of Sri Lanka. Four methods were used: visual census using video, photographs, stationary point count and environmental DNA (eDNA). A total of 137 fish species, 74 coral species and 175 other species were recorded using the four methods. There were similarities and differences between the methods for recording fish, corals and other species. Only three fish species: Moon wrasse (Thalassoma lunare); Yellowtail fusilier (Caesio cuning) and Diamond fish (Monodactylus argenteus) were recorded by all methods. The highest number of fish species was recorded by video, followed by photographs, eDNA and stationary point count in the sequence. Coral cover ranged from 9 to 50.8% and mean live coral varied from 24.4% to 34.5 ± 5.2%. The dominant coral species was Pocillopora damicornis. Rare observations of coral bleaching (n=1) and frequent observations of marine debris (n=20) and coral damage (n=25) were recorded. Species detection using eDNA is a biomonitoring tool that did not add significantly to the list of fish and corals, but included many microscopic groups such as bacteria, diatoms and ciliates that were not recorded using other methods, and provided new ecological insights into marine systems. This is the first use of multiple monitoring tools to identify and compare methods for the biodiversity of marine fish, coral and other species in Sri Lankan marine waters.

Continual Day–Night eDNA Detectability Amidst Diel Reef Species Fluctuations on Diver Transects

ABSTRACTRecent research into the spatiotemporal dynamics of eDNA in marine environments indicates that eDNA signals are highly localized and may dissipate beyond detection levels within a few hours of production. This affects whether single‐timepoint eDNA sampling, which generally occurs during daylight hours, or cyclic (day/night) interval eDNA sampling is necessary to detect both diurnal and nocturnal marine species. Our study investigated short‐term variability in eDNA derived from fishes and macroinvertebrates across three temperate reef sites in eastern Tasmania, Australia. Simultaneous eDNA and underwater visual census (UVC) diver transect surveys were conducted every 6 h over a 24‐h period to investigate whether eDNA was able to detect marine species outside of their UVC‐observed diel activity. We report that single‐timepoint eDNA sampling can detect both diurnal and nocturnal species on temperate reefscapes. A lack of eDNA compositional turnover between day and night suggests that eDNA persists beyond 12 h and/or is continuously produced by both diurnal and nocturnal reef taxa, irrespective of diel behavioral changes observed by UVC. Given high eDNA sample variability, however, we recommend a high replication level (> 10 × 1 L samples) to produce robust site community composition profiles. This study builds on emerging literature on short‐term variability in eDNA, assisting in the design of future eDNA studies at sites with pronounced variation in faunal activity between day and night.

Sandy bottoms have limited species richness but substantially contribute to the regional coastal fish β-diversity: A case study of the Central Mediterranean Sea

Global marine biodiversity loss impairs entire ecosystems and their stability. Robust biodiversity estimates are key to inform policies and management strategies, and need to consider the contribution of diverse habitats, including those for which estimates of biodiversity are scattered or totally absent. This study assessed the fish diversity associated with three main coastal habitats (rocky bottoms, Posidonia oceanica meadows, sandy bottoms), and their role in shaping the overall coastal fish diversity, also in relation to potential environmental and anthropogenic drivers affecting patterns of fish diversity in coastal areas. Using underwater visual census, we sampled 62 sites distributed on the three habitats, for a total of 496 replicates. We assessed the contribution of each habitat to β-diversity, divided into Local Contribution to β-diversity (LCBD), a comparative indicator of the contributions to β-diversity of each habitat, and Species Contribution to β-diversity (SCBD), which measures the relative importance of each species in affecting β-diversity. Finally, we modelled species diversity in relation to potential environmental and anthropogenic drivers. Overall, 72 species were recorded, with the highest species richness observed on rocky bottoms (56 species, 16 unique to this habitat), followed by P. oceanica (38 species, 0 unique) and sandy bottoms (32 species, 14 unique). Sandy bottom assemblages had a significantly higher contribution to LCBD than P. oceanica meadows and rocky bottoms, and two of the five species with the highest contribution to SCBD are exclusively associated with sandy bottoms. Finally, sea surface temperature, sea surface salinity, and habitat were highlighted as significant predictors of species richness. Our findings, aside from highlighting the environmental drivers of coastal fish diversity in the Mediterranean Sea, unravel the potential key role of sandy bottoms in contributing to overall coastal fish diversity and can inform conservation planning.

Broken expectations: Population decline of a key grouper species within a 30-year-old no-take MPA in the Southwestern Atlantic

Understanding the impacts of human actions on marine species and developing mitigation strategies are crucial conservation challenges. Many fish species, especially marine top predators, are already highly depleted and rely on population monitoring and conservation strategies for their maintenance. In this context, Marine Protected Areas can help recover target species and provide crucial information about population trends when human activities are restricted or managed. Here, we used the longest and most complete temporal series of reef fish data in the Southwestern Atlantic, comprising 16 years of underwater visual census sampling. We evaluated temporal trends in the density and biomass of the dusky grouper (Epinephelus marginatus), both inside and outside a no-take and no-entry Marine Reserve. Our findings reveal a consistent decline in density and biomass inside and outside the MPA over time, reaching alarmingly low densities and experiencing a steeper biomass decline in the last five years. Our results contradict global expectations of positive population recovery trends within MPAs. We highlight the adverse impacts of human activities on the dusky grouper population, including illegal fishing and habitat degradation. Additionally, we address the limited understanding of species' life stages, underscoring that their occurrence outside protected boundaries may render the entire population vulnerable to human pressures. Thus, to guarantee population recovery, stakeholders and researchers must take immediate action to increase knowledge of all life stages and improve ongoing strategies.

Habitat-specific response of fish assemblages in a small fully protected urban MPA

Abstract This study aims at assessing the reserve effect on fish assemblage in a small urban fully protected and highly enforced Marine Protected Area (MPA), Larvotto MPA (Monaco, Mediterranean Sea). The data about fish density, size, and biomass was collected by underwater visual census in the MPA and unprotected areas in two habitats, artificial rocky substrates and Posidonia oceanica meadows. On artificial rocky substrates, we recorded significantly higher fish biomass within the MPA compared to unprotected areas, while no significant difference was detected on Posidonia, with this suggesting the habitat-specific responses of fish assemblages to protection. Here we highlight the potential effectiveness of highly enforced small-sized urban MPAs, such as the Larvotto MPA, in generating ecological benefits, and speculate about their potential role in supporting networks of MPAs. This study supports increased attention to urban MPAs in conservation efforts, emphasizing the need for efficient management strategies in the face of ongoing coastal expansion.

The distribution of coral reef fish biodiversity on Bontosua Island, Spermonde Archipelago, South Sulawesi Province

Background: Bontosua Island, located in the Spermonde Archipelago, is one of the strategic and historical islands in the region. The island plays a vital role in ecosystem conservation efforts by the local community, who are committed to preserving their natural environment. With dynamic ecosystem conditions, it is essential to understand the seabed cover and biodiversity on the island to support more effective conservation efforts. Methods: This study was conducted from March to September 2022 to mark the seabed cover of Bontosua Island and understand the relationships between coral reef fish species and the ecosystem. The method used was a stationary visual census, followed by descriptive analysis and one-way ANOVA to assess the biodiversity and diversity of coral reefs. Findings: The results showed a total of 1,306 coral reef fish from 9 families with 63 species identified, including the families Chaetodontidae, Serranidae, Lutjanidae, Haemulidae, Lethrinidae, Scaridae, Acanthuridae, and Siganidae. The families with the highest citations were Scaridae, Acanthuridae, and Siganidae. The highest coral reef fish were found in the north, west, and southwest of the island, where live coral areas are more dominant. Conclusion: This study shows that Bontosua Island has significant coral reef diversity, and certain areas, such as the north and southwest sides, have higher reported fish. These findings indicate the importance of these areas in conservation efforts. Novelty/Originality: This study provides a comprehensive picture of the seabed cover and coral reef fish diversity in Bontosua Island, which has yet to be widely discussed in previous studies. These findings provide a scientific basis for more targeted conservation strategies and help improve understanding of the dynamics of coral reef ecosystems in the Spermonde Islands.. Novelty/Originality of this article: This study proposes developing a community-based coral reef monitoring system that integrates local knowledge with digital mapping technology, aiming to increase the effectiveness of conservation and management efforts of marine resources on small islands.

Community Structure of Fishes at Coral Reef Ecosystem in Pandanan Beach, Northern Lombok, West Nusa Tenggara

One of the most abundant kinds of organism that lived in coral reef ecosystem are fish. Fish rely on coral reefs for shelter, food, and breeding grounds. Lombok is one of the islands that have many hotspots of coral reef ecosystem, one of which is at Pandanan Beach. The precense of fish benefits in both tourism and local economy, however the data about reef fish that lived in Pandanan waters are less known. This research aimed to assess the community structure of fish species in coral reef ecosystem at Pandanan Beach. The method that was used for sampling were UVC (Underwater Visual Census) with BIT (Belt Intercept Transect) technique at three different stations. The results showed 554 individuals which consist of 34 species from 12 families had been identified. The community structure of fish in the three stations showed the moderate level of diversity, stable evenness index with low dominance, and density value of 0,73. Environmental parameters measurement indicate Pandanan waters are suitable for fish growth and survival.

Kelimpahan dan Biomassa Ikan Karang di Kawasan Konservasi Perairan Gili Balu, Kabupaten Sumbawa, Nusa Tenggara Barat

The Gili Balu Marine Conservation Area (KKP), located in Sumbawa Regency, West Nusa Tenggara, is ecologically and economically significant due to its rich coral reef ecosystems. This research aims to measure the abundance and biomass of reef fish in the KKP Gili Balu, which can be used as a basis for evaluating the effectiveness of conservation efforts in maintaining marine biodiversity. The Underwater Visual Census (UVC) method was used, recording types of reef fish at ten observation points. The results showed that the highest abundance was found on Mandiki Island, with functional fish abundance reaching 2973 ind/ha, followed by Pasareang Barat Island (1903 ind/ha) and South Kalong (1600 ind/ha). The biomass of functional fish also reflects their important role in maintaining the balance of the coral reef ecosystem. This research contributes to the scientific understanding of marine biodiversity in the KKP Gili Balu and provides a basis for sustainable conservation management efforts. Additionally, the research recorded the presence of several coralivorous and economically important fish species, although they tend to be smaller compared to functional fish. Economically important fish in the KKP Gili Balu waters were found only at four observation locations: East Belang Island, North Belang, Kenawa, and Southwest Namo. The highest value was recorded at Kenawa Island, with 93 ind/ha. These fish tend to be rare in this area, possibly due to past fishing practices.

Application of eDNA metabarcoding in the assessment of fish biodiversity in Philippine mangroves: Challenges and opportunities

Biodiversity assessments are important in designing mangrove conservation and restoration programs. In the Philippines, conventional biodiversity assessment methods (e.g., trap nets, fish visual census) can be time-consuming, labor-intensive, and expensive. In recent years, environmental DNA (eDNA) metabarcoding has been an emerging tool for rapid biodiversity monitoring as it is fast, non-intrusive, and can provide broader detection of fauna. But, it is still subject to various field sampling and laboratory analysis constraints. Here, we applied the eDNA metabarcoding method to document and assess fish biodiversity in mangroves from two biogeographic regions in the Philippines: Oriental Mindoro in the West Philippine Sea and Sorsogon in the Northern Philippine Sea. Using 12S genetic markers from eDNA water samples, we detected 89 fish species from 44 families. Only twelve species were commonly detected in both sites. Several species were found in the Philippines’ list of economically important aquatic organisms while one species (Epinephelus fuscoguttatus) was classified as Vulnerable in IUCN’s Red List of Threatened Species. Seventy-six percent more species were detected in Sorsogon probably because the sampling sites were within a seascape of mangroves, seagrasses, and coral reefs. In contrast, the lesser species detected in Oriental Mindoro could probably be because of the more limited sampling points to coastal fringes. Our results serve as baseline data and the first obtained using this method in the country. However, we observed some limitations that should be addressed to improve the method: (1) lack or absence of a comprehensive reference database specific to Philippine aquatic organisms; (2) low eDNA reads which could be attributed to insufficient on-site filtration due to turbid seawaters common in Philippine mangroves; and (3) possible cross-contaminations that can affect comparative analyses. Despite these limitations, we were able to demonstrate the usefulness of this technique in doing rapid assessments which could address knowledge gaps in Philippine mangrove biodiversity studies and contribute to its conservation programs.