Serranilla is a protected island of the Seaflower Biosphere Reserve, far from dense human population. These characteristics could help sustain structurally complex coral reefs, often associated with higher biodiversity, abundance, and biomass of reef-associated organisms, including reef fish. However, the multiple threats present in Serranilla, including intense illegal fishing, can impact coral ecosystems generally and also specific key groups, such as the parrotfish, in particular. During the “Seaflower Research Expedition 2017”, we assessed how structural habitat complexity influences reef fish assemblages. In addition, we explored differences in parrotfish species (family: Scaridae) between Serranilla and San Andrés, the most populated island in the Archipelago. On Serranilla, we found that habitat structure, rugosity, and coral cover accounted for up to 66% of variation in reef fish diversity, abundance, and biomass, with values being higher on more complex reefs. Parrotfish species differed between the islands, with larger species supporting higher biomasses at Serranilla, by comparison with San Andrés; however, the abundance, biomass, and lengths of parrotfish species were low in both areas compared with those reported from other protected Caribbean reefs. Our study indicates that despite the evident relationship between structurally complex habitats and reef fish, other threats in Serranilla could be affecting parrotfish populations, such as illegal fishing, a widespread activity in the area.