Marine Biodiversity Hotspot Research Articles

Changes in biogeographic patterns of coastal benthic decapods: Indicators of tropicalization in the Canary Islands over the last 50 years

The Canary Islands constitute one of the major marine biodiversity hotspots in the eastern-central Atlantic, with decapod crustaceans being a highly representative group in the benthic environment due to their vast diversity of taxa and occupied ecosystems. This study identifies three significant milestones corresponding to the publication of comprehensive decapod checklist for the Canary Islands in 1973, 1995, and 2018. The lists of coastal benthic decapod species (0–300 m depth) were revised and updated, indicating the biogeographic pattern and vertical distribution range of each species in the region. Changes in the composition of the biogeographic patterns of coastal decapods in the Canary Islands were analysed to evaluate whether they could be considered as a useful indicator of the tropicalization process in the region. Particular attention was paid to variations in the percentages of species with warm water affinity versus those with Atlanto-Mediterranean preferences, with the former showing a clear upward trend.

Fine-scale phylogeography of Tripneustes gratilla revealed a core-periphery pattern in the South China sea

The Core-Periphery Hypothesis (CPH) is a theoretical framework in phylogeography used to examine the spatial distribution of genetic diversity. The tropical Indian-Western Pacific (IWP), serving as a prominent marine biodiversity hotspot, constantly exports species and evolutionary novelties to peripheral habitats. Many species display genetic patterns consistent with CPH predictions from the IWP to periphery regions. However, the presence of CPH’s genetic signals in intermediate distribution zones remains underexplored. Here, we collected four sea urchin populations of Tripneustes gratilla in the South China Sea and analysed their population structure and evolutionary patterns using 13 morphological parameters, one mitochondrial 16S rRNA gene and nine polymorphic microsatellites. The results revealed substantial genetic homogeneity among the populations, implying a single origin from a glacial refugium. Nonetheless, morphological and microsatellite data distinctly differentiate the northernmost Fengjiawan population from the others, which could be attributed to increased environmental selection pressures such as temperature. Analysis of genetic diversity variation along latitudinal gradients and the relationship between geographic and genetic distances align with CPH expectations for both 16S and microsatellites, albeit to varying degrees of significance. This study enhances our understanding of tropical marine invertebrate evolution and supports the applicability of the CPH model at a fine-scale level.

Satellite observed oceanographic drivers of Mobulidae fisheries catch in the Southeast Indian Ocean

Indonesian coastal waters include several marine megafauna biodiversity hotspots. Several fish populations of ecological and socio-economic importance, such as elasmobranchs (sharks and rays), have experienced rapid decline due to unsustainable human activities, primarily overfishing. Small-scale fisheries (SSF) are currently exempt from governmental fisheries management measures despite contributing a significant proportion of a total catch. The Generalised Additive Models were used to investigate the effect of variations in oceanographic parameters of the Teluk Penyu fishing ground, south of central Java, on the magnitude of Mobulidae (Mobula spp.) catch based on its landings data over ten years (2009–2018) from one of Indonesia's largest ports, Cilacap, Central Java, Indonesia. Mobulidae catch from Teluk Penyu fishing ground was generally higher from June to November when the water exhibited relatively high sea surface salinity (sal >34.1 ‰), chlorophyll (0.32–0.45 mg/m3), and nitrate (nit >0.0045 mg NO3/m3), water speed (>0.29 m/s) and eddy kinetic energy (>0.04 m3/s2) levels, and relatively low sea surface temperature (<28 °C), oxygen (<0.182 mg O2/m3) and sea surface height (<0.9 m) levels than the other months of the year. This study reveals that satellite Earth Observation (EO) data provided a preliminary relationship between oceanographic conditions and the amount of catch for developing more effective management and conservation measures for endangered species like Mobulidae. Utilizing EO data may also be applied to help inform much-needed ecosystem-based management measures, including habitat protection and bycatch reduction for conserving endangered Mobulidae species in the Southeast Indian Ocean. The in-situ onboard ocean observation and temporal species-specific catch data will greatly complement the current work.

Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity

Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world’s coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.

A Comparison between the Production of Edible Macroalgae Worldwide and in the Mediterranean Sea

Macroalgae are beneficial for consumers and producers due to their high productivity, their chemical composition and their efficient cultivation without additional feed. Asia dominates global macroalgae production, while European production is still marginal and mainly based on wild harvesting in the North Atlantic. The European Commission has launched initiatives to promote the sustainable production, safe consumption and innovative use of macroalgae products in European regional seas, including the Mediterranean Sea. A variety of coastal and seabed types and a wide range of environmental conditions make the Mediterranean a hotspot of marine biodiversity while providing good conditions for the cultivation of macroalgae. The aim of this paper is to compare the global macroalgae production and macroalgae production in the Mediterranean Sea, focussing on the cultivation of edible macroalgae. The paper also discusses the limitations and possibilities of macroalgae production in the region. Macroalgae production is one of the most promising sectors of the blue economy in the Mediterranean. The production of edible macroalgae suitable for human consumption has great potential, considering future population growth and related food security and health issues, as well as the additional ecosystem benefits of macroalgae production.

An ecological coherence assessment of the Wider Caribbean Region marine protected area network

Marine protected areas (MPA) are area-based management tools that serve as the cornerstone for marine conservation and sustainable use. There has been a recent shift from establishing MPAs on an individual basis to establishing networks of connected MPAs to better reflect the transient dynamics of marine species and to ensure they are acting synergistically to deliver their intended outcomes in a coherent manner. This study employs innovative geospatial analysis to assess the ecological coherence of the MPA network comprising 846 sites within the Wider Caribbean Region, a global hotspot of marine biodiversity. Evaluating four main criteria widely used in policy—representativity, replicability, connectivity, and adequacy—through 14 tests, our findings indicate that the current MPA network is unlikely to have achieved ecological coherence across all criteria. To improve ecological coherence, regional management could focus on expanding coverage of ecologically important areas, encompassing a broader range of biogeographic zones, and protecting the full spectrum of marine habitats in the region. Efforts should also be directed towards establishing larger MPAs and increasing the number of MPAs with no-take zones, while ensuring the protection of indigenous and local communities' rights to sustainable marine resource use.

Fisher’s perceptions on shark fisheries in Sao Tome Island (Gulf of Guinea, West Africa)

Sao Tome and Principe (STP) is a small island developing state in the Gulf of Guinea (West Africa) and is considered a global hotspot of marine biodiversity. Still, detailed information on sharks’ diversity, abundance, and respective fisheries is mainly absent. Here, we interviewed fishers from different local communities of the island of Sao Tome to characterize: i) local knowledge on shark fisheries, ii) those reliant upon these resources, and iii) their perceptions about shark populations and their importance on Sao Tome Island. A total of 111 semi-structured interviews were conducted between May 6 and June 15, 2019, in 11 fishing communities. Ninety-seven percent of fishers mentioned that sharks are present in their fishing grounds, and 98 % reported that they catch sharks. The species most identified by fishers (77 %) was the scalloped hammerhead shark (Sphyrna lewini), followed by the bluntnose sixgill shark (Hexanchus griseus; 33 %), white shark (Carcharodon carcharias; 31 %), longfin mako shark (Isurus paucus; 29 %), pigeye shark (Carcharhinus amboinensis; 27 %), and other six species (under 20 % each). Sixty-two percent of interviewees perceived sharks as a threat to their safety and livelihoods. When asked if sharks should be protected, 59 % of fishers agreed, while 40 % did not consider it necessary. Common reasons in support of protection were that sharks were disappearing (23 %), important for ocean health (9 %), and overfished (5 %). Most fishers (89 %) noticed shark abundance changes, decreasing over the past 15 years. Regarding the underlying causes, the most common response was the increase in the fishing pressure from international fishing fleets (72 %). We argue that raising awareness and building capacity close to local communities on sharks' essential role and importance will be fundamental to supporting future conservation measures, as misinformation and prejudice against sharks are widespread.

Cenozoic history of the tropical marine biodiversity hotspot

The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation–extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.

Biodiversity of Nematodes from Coral Reef Sediments in the South China Sea Based on eDNA Metabarcoding

Coral reef ecosystems in the South China Sea are one of the globally important marine biodiversity hotspots. However, there are few studies on nematode biodiversity in coral reef sediments. Here, we assessed nematode biodiversity in coral reef sediments in the South China Sea using eDNA metabarcoding. Eight sampling stations were set up in the region north of the South China Sea Basin (Xisha and Zhongsha Islands) and south of it (Nansha Islands), respectively. We also compared and analysed the nematode biodiversity and community structure in different regions, as well as the effects of environmental factors on the community structure. The results showed that a total of 503 operational taxonomic units (OTUs) were detected in 16 sediment samples. The nematodes identified belong to two classes, 10 orders, 37 families, 51 genera and 61 species, and all of them were Enoplea and Chromadorea, except for the unidentified taxa, which accounted for 97.26% of the total abundance. The analyses showed that the northern region had higher nematode abundance and diversity relative to the southern region. However, there was no significant difference in the nematode community structure between the two regions, which was less affected by geographic location. Similarly, environmental factors (total nitrogen, total phosphorus, copper, zinc, cadmium, lead and arsenic) have an effect on the abundance of specific nematode groups but not on the overall community structure. In summary, this study initially reveals the composition and diversity of nematode communities in coral reef sediments in the South China Sea and provides an important reference for further in-depth study of the South China Sea ecosystem.

First Record of the Red Cornetfish Fistularia petimba Lacepède, 1803 from Amorgos Island (Central Aegean Sea; Greece) and a Review of Its Current Distribution in the Mediterranean Sea

The rapid spread of non-native species (NNS) poses a significant threat to biodiversity globally, with the Mediterranean region being particularly susceptible due to increased human activities and its status as a marine biodiversity hotspot. In this study, we focus on the introduction and distribution of Fistularia petimba, a member of the Fistulariidae family, in the eastern Mediterranean Sea and a record from the coasts of Amorgos Island, Greece. Through a baseline fishery study conducted over 12 months, utilizing experimental sampling with gillnets, trammel nets, and longlines, one individual of F. petimba was captured off the coast of Katapola Bay. Morphological examination confirmed its identity, with measurements on meristic characteristics obtained and the stomach content analysed. This finding represents a significant addition to the documented distribution of F. petimba in the Mediterranean Sea, particularly in the Aegean Sea, underscoring the importance of ongoing research in uncovering new occurrences and expanding our understanding of marine biodiversity and ecosystem changes. Further investigation into the ecological preferences and population dynamics of F. petimba in the Aegean Sea is crucial for informed conservation and management efforts if this species is considered to be established.

Healthy assemblages of Isidella elongata unintentionally protected from trawling offshore of Asinara Island (northwestern Sardinia, NW Mediterranean Sea)

Deep-sea coral assemblages are marine biodiversity hot spots. Because of their life history traits, deep-sea corals are highly vulnerable to the impacts of human activities such as fishing. The critically endangered “bamboo coral” Isidella elongata is a key structuring species of deep muddy bottoms that is susceptible to habitat destruction, particularly from trawling. A shallow population of this species was recently discovered by a multibeam and ROV survey offshore of the Asinara Island marine protected area (MPA) (northwestern Sardinia, NW Mediterranean Sea). This vulnerable marine assemblage has been found under healthy conditions at depths ranging from 110 to 298 m. Isidella elongata occurs on a muddy seafloor locally characterised by boulders associated with black coral species (Parantipathes larix and Antipathes dichotoma). The lush colonies of I. elongata seem to be related to natural protection from bottom trawling activity; nevertheless, the presence of lost fishing artisanal nets has been observed in the study area. These structuring species are indicators of vulnerable marine ecosystems, and their conservation is essential for preserving marine biodiversity. Therefore, enlarging the perimeter of the Asinara Island MPA into its deeper western waters is suggested to ensure the protection of these valuable and vulnerable marine ecosystems.

Arctic puzzle: Pioneering a northern shrimp (Pandalus borealis) habitat model in Disko Bay, West Greenland

Recent advancements in spatial modelling leverage remote sensing data and statistical species-environment relationships to forecast the distribution of a specific species. Our study focuses on Disko Bay in West Greenland, recognized as a significant marine biodiversity hotspot in the region. We conducted comprehensive analyses using multiple datasets spanning from 2010 to 2019, incorporating shrimp and fish surveys, commercial shrimp fishery catches, high-resolution (25 × 25 m) multibeam bathymetry and backscatter data along with a medium-resolution (200 × 200 m) bathymetric model, measured and modelled oceanographic data, and satellite chlorophyll data. Through multivariate regression analysis, we tested the significance of various physical factors (seafloor depth, sediment class, bottom water temperature, bottom water salinity, bottom current velocity, space, and time), biological factors (chlorophyll a, Greenland halibut (Reinhardtius hippoglossoides)), and anthropogenic impact (shrimp fishery; standardized catch per unit effort) on the density of northern shrimp in the area. Our results indicate a significant association between northern shrimp density, seafloor depth, and sediment class, explaining 36 % of the variation in shrimp density. Subsequently, we developed a high-resolution (optimized) spatial linear mixed–effect model to map the distribution of northern shrimp across Disko Bay, representing the first model of its kind developed for an Arctic area. The optimal habitat for northern shrimp is characterized by medium-deep waters (approximately 150–350 m), turbulent conditions, and mixed sediments, predominantly located in the northern and southern regions of Disko Bay. Notably, the northern region hosts a relatively diverse benthic community, with northern shrimp and sponges as the primary contributors of epibenthic biomass. This novel high-resolution model significantly enhances our understanding of the physical drivers and detailed spatial patterns influencing the distribution of northern shrimp in the Arctic.

Recent record of True Giant Clam Tridacna gigas from the Sulu Archipelago and insight into the giant clam fisheries and conservation in the southernmost islands of the Philippines

The Philippines is a hotspot for marine biodiversity, particularly for giant clams like Tridacna gigas. Despite protective measures, giant clams are threatened with extinction due to overharvesting and habitat loss. We conducted a rapid documentation of a rampant giant clam fishery and trade we discovered in Panggungan Island in Sitangkai, Tawi-Tawi during our assessment, following a ship grounding incident in the area. We observed numerous empty shells of various giant clam species scattered across the area, indicating active harvesting by the community. The locals sell the meat, either fresh or dried and pearls collected from giant clams. The local community culture live with giant clams, including the true giant clam species, Tridacna gigas, along the shorelines. The largest live T. gigas individual we documented had a shell length of about 60 cm. Our study provides the first documentation of wild adult T. gigas in the Sulu Archipelago. It is also the only report of sighting of wild adult T. gigas aside from Palawan. Furthermore, our study marks the first account of giant clam trade within the Philippines since the early 1980s when the government issued a total ban on catching and selling of all species giant clams. Our findings highlight the critical need for a thorough assessment of T. gigas and other giant clam species in the biodiversity-rich Sulu Archipelago. Effective conservation of giant clams and the surrounding reefs will ensure the future of our marine ecosystems and the communities that rely on them.

Response of Mediterranean Sea bivalves to Pliocene–Pleistocene environmental changes

AbstractThe Mediterranean Sea is recognized as a hotspot of marine biodiversity. Analysing its past biodiversity can help in understanding species' response to climate change. We built a species‐level dataset of bivalve occurrences across the Zanclean–Calabrian interval, a time characterized by significant changes in climate, and by bivalve extinctions. The dataset includes more than 400 species distributed from the eastern to the western Mediterranean Sea. We measured changes in richness and turnover through time, for the entire dataset, and for different palaeoenvironments and combinations of tiering and feeding categories to test if specific environmental conditions and different lifestyles were correlated to species extinction or survival through time. We also compared niche breadth, geographical range size, and species abundance of extinct and extant species, to test which of these parameters potentially affected extinction risk. Our results confirm a loss of biodiversity between 3 Ma and the Early Pleistocene, although this loss was less intense and more gradual than previously estimated. We also found significant differences in niche breadth and geographical range size between extinct and extant species. Suspension feeders lost a higher proportion of species and suffered a higher reduction of geographical range compared to infaunal deposit feeders. Species loss was more protracted and higher on the shoreface than on the shelf, which is probably related to the reduction of shallow‐water vegetated environments and to the disaggregation of heterozoan carbonate ramp habitats with cooling and sea‐level drop at the onset of the northern hemisphere glaciation.

Historical ecology of pinnipeds of the northern coast of the San Jorge Gulf (central Patagonia, Argentina) since the Late-Holocene

The northern coast of the San Jorge Gulf, Atlantic Patagonia, is recognised as a marine biodiversity hot spot and is designated as a priority conservation area. Among marine mammals, three species of pinnipeds inhabit the region. While South American sea lions ( Otaria flavescens) have a higher abundance and a larger number of colonies than South American fur seals ( Arctocephalus australis), a few individuals of the Southern elephant seal ( Mirounga leonina) reside in the region. Nevertheless, little is known about the abundance and distribution of these pinnipeds before the 18th century, when various extractive activities became widespread, including the unregulated exploitation of furs and oil. This study aims to examine whether the distribution and relative abundance of ancient pinnipeds differ from present-day populations. To achieve this, we conducted inter-specific identification of pinniped bone remains coming from archaeological assemblages dated from 6000 to 600 14C years BP and reviewed historical sources to contrast these retrospective data with modern ecological literature. The results suggest changes over time in the relative abundances of species within the pinniped community. The relative abundance of fur seals was greater than or equal to that of sea lions in most Late-Holocene pinniped assemblages. Additionally, fur seals have been recorded in historical and Late-Holocene periods in places where they are currently very rare. These findings are consistent with the higher relative abundance of fur seals recorded in other archaeological sites along the Patagonian coast, suggesting that modern distribution and abundance have been heavily affected by commercial hunting. This study contributes to a better understanding of the nature and magnitude of the anthropic impact on the marine ecosystem of the northern coast of the San Jorge Gulf. It also provides historical baseline information to strengthen conservation policies and restoration efforts.

Genetic structuring and species boundaries in the Atlantic stony coral Favia (Scleractinia, Faviidae)

AbstractScleractinian corals are the main modern builders of coral reefs, which are major hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo‐Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi‐Atlantic hard coral genus Favia. Coalescent‐based species delimitation (BFD* – Bayes Factor Delimitation) recovered F. fragum and F. gravida as separate species. Although our results agree with depth‐related genetic structuring in F. fragum, they did not support incipient speciation of the ‘tall’ and ‘short’ morphotypes. The preferred scenario also revealed a split between two main lineages of F. gravida, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were corroborated by analyses of SNP matrices with varying levels of missing data and by a speciation‐based delimitation approach (DELINEATE). Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in Favia and rejected the long‐standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations.

EDNA-based survey of the marine vertebrate biodiversity off the west coast of Guadeloupe (French West Indies).

In the marine environment, knowledge of biodiversity remains incomplete for many taxa, requiring assessments to understand and monitor biodiversity loss. Environmental DNA (eDNA) metabarcoding is a powerful tool for monitoring marine biodiversity, as it enables several taxa to be characterised simultaneously in a single sample. However, the data generated by environmental DNA metabarcoding are often not easily reusable. Implementing FAIR principles and standards for eDNA-derived data can facilitate data-sharing within the scientific community. This study focuses on the detection of marine vertebrate biodiversity using eDNA metabarcoding on the leeward coast of Guadeloupe, a known hotspot for marine biodiversity in the French West Indies. Occurrences and DNA-derived data are shared here using DarwinCore standards combined with MIMARKS standards.

Molecular genetic biodiversity assessment of the Wallis Island sponge fauna in the Tropical Pacific

Abstract Polynesia is a hotspot for marine biodiversity in the South Pacific Ocean, yet the distribution of many invertebrate taxa in this region is still often poorly assessed. Information on the diversity and phylogeography of sponges in particular remains limited in spite of their importance for coral reef ecosystems. Recent expeditions to the island group of Wallis and Futuna enabled the first larger-scale assessment of the Wallis Island sponge fauna, resulting in the molecular identification of 82 unique Molecular Operational Taxonomic Units (MOTUs) from 339 sponge samples based on 28S C-region rDNA and CO1 mtDNA data. Faunal comparisons with both adjacent archipelagos and more distant Indo-Pacific regions were predominantly based on the MOTUs obtained from Wallis Island ecoregions, and suggest high levels of endemism of sponges in Wallis and Futuna, corroborating previous data on the biodiversity of sponges and other marine phyla in the South Pacific. The results of this molecular taxonomic survey of the Wallis and Futuna sponge fauna aim to lay solid foundations for a sustainable ‘Blue Economy’ in Wallis and Futuna for the conservation of their local coral reefs.

Research trend on marine zooplankton in Indonesian Waters: A systematic review

Research on marine zooplankton in Indonesian waters was conducted in the 19th century. However, there is limited information regarding evaluating the research trends and notable scientists involved in this area. This study aims to know the research trend on marine zooplankton research in Indonesian waters. This study analyzed publications that were included in the Scopus database from 1900 to 2021. A systematic review was undertaken using a three-stage procedure including identification, screening, and final following PRISMA chart. The final list was analysed in terms of topics of research, keywoards, location, time of publication, and authorship.. We found that the research trend was changed. During the early stages of the study, there was a prevalent focus on studying both taxonomy copepods and parasite Copepods. However, in recent times, there has been a shift towards favoring the plankton ecology. Despite being a hotspot for marine biodiversity, Indonesia only had a few taxonomists, therefore it was overlooked when marine zooplankton was discovered in its seas. We also found that most of the new finding species come from copepods whereas the other taxa of zooplankton remain undescribed or misidentification. Additionally, young scientists pay less attention to the study of taxonomy. To address these problems, priority is given to intensive training for early-career scientists. Comprehensive approaches using morphological traits and genetic tools will solve this issue.

DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub.

The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next-generation monitoring. With this objective, we present the results of a large-scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA-based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.