Predatory and large-bodied coral reef fishes have fundamental roles in the functioning and biodiversity of coral reef ecosystems, but their populations are declining, largely due to overexploitation in fisheries. These fishes include sharks, groupers, Humphead wrasse (Cheilinus undulatus), and Green Humphead parrotfish (Bolbometopon muricatum). In the western Indian Ocean, this situation is exacerbated by limited population data on these fishes, including from conventional visual census methods, which limit the surface area surveyed. We developed a rapid timed scuba swim survey approach for application over large areas for estimation of the abundance of large-bodied reef fishes and assessment of the effectiveness of marine protected areas (MPAs) in maintaining these species’ populations. Using this method, we sampled 7 regions in the western central Indian Ocean and
Gulf of Aden, including 2 remote reference locations where fishing is prohibited. Eight
families were selected for the surveys from across 3 categories: pelagic, demersal, and large-bodied single species. Sharks (Carcharhinidae) were absent in 5 of the 7 regions, observed only in Mozambique and the Chagos Archipelago. Tunas (Scombridae) and barracudas( Sphyraenidae) were rarely observed (none in Madagascar, Djibouti, and Iles Glorieuses). The Giant grouper (Epinephelus lanceolatus) was absent in all regions, Humphead wrasse was absent in Comoros and Iles Glorieuses, and Green Humphead parrotfish was observed at only one site in Tanzania. The MPAs were not effective in protecting these single large-bodied species or the 4 pelagic families, except for sharks in the highly protected reference ocations. However, MPAs with medium levels of protection were effective in maintaining the abundance of some demersal families, notably large-bodied groupers. Our results support the hypothesis of local extirpation of these large-bodied fishes on many coral reefs in the western Indian Ocean.