Communities of coral reef fishes are changing due to global warming and overfishing. To understand these changes and inform conservation, knowledge of species diversity and distributions is needed. The western Indian Ocean (WIO) contains the second highest coral reef biodiversity hotspot globally, yet a detailed analysis of the diversity of coral reef fishes is lacking. This study developed a timed visual census method and recorded 356 species from 19 families across four countries in the WIO to examine patterns in species diversity. Species richness and composition differed most between the island countries of Madagascar and Comoros and both these locations differed from locations in Tanzania and Mozambique which were similar. These three regional groupings helped define WIO ecoregions for conservation planning. The highest species richness was found in Tanzania and Mozambique, and the lowest and most different species composition was found in Comoros. Biogeography explains these differences with naturally lower species diversity expected from the small, oceanic, and isolated islands of Comoros. Present day ocean currents maintain these diversity patterns and help explain the species composition in northeast Madagascar. Species distributions were driven by 46 of the 356 species; these provide guidance on important species for ongoing monitoring. The results provide a benchmark for testing future changes in reef fish species richness.