Benthic habitat composition is a key factor that structures assemblages of coral reef fishes. However, natural and anthropogenic induced disturbances impact this relationship. This study investigates the link between benthic habitat composition and fish functional groups in four countries in the Western Indian Ocean (WIO). Benthic composition of 32 sites was quantified visually from percentage cover of hard and soft corals, rubble, turf, fleshy and crustose coralline algae. At each site, abundance of 12 coral-associated fish functional groups in 50 × 5 m transects was determined. Cluster analysis characterized reefs based on benthic cover and revealed five habitat types (A, B, C, D and E) typified by decreasing cover of hard corals, increasing cover of turf and/or fleshy algae and differences in benthic diversity. Habitat type A was present in all four countries. Other habitats types showed geographic affiliations: notably Comoros sites clustered in either habitats B or E, northern Madagascar had B, C and D type habitats, whereas sites in central Tanzania and northern Mozambique had habitats D and E. Fish functional groups showed significant linkages with some habitat types. The abundances of corallivores, invertivores, detritivores and grazers were higher in habitat B, whereas planktivores and small excavators showed lower abundances in the same habitat. These linkages between benthic habitat types and fish functional groups are important in informing priority reefs that require conservation and management planning.