Spatial distribution of coral reef fishes is related to diverse environmental variables. This study aimed to elucidate the (1) broad-scale spatial distribution, (2) microhabitat-scale substrate association, (3) degree of dependence on live corals and (4) habitat partitioning of 26 damselfish species on an Okinawan coral reef. Broad-scale analysis revealed that fish assemblages could be divided into three groups in relation to the degree of wave exposure, and the coverage of live corals as well as non-coralline substrates: (1) 11 species that were found in exposed reefs with greater coverage of rock
(2) nine species that that were found in inner reefs with greater coverage of live corals, dead corals and macroalgae
and (3) six species that were found in inner reefs with a greater coverage of sand. Microhabitat-scale analysis revealed that fish assemblages could be divided into six groups in relation to diverse microhabitat availability: (1) 12 species showed significant positive associations with rock
(2) two species showed significant positive associations with coral rubble
(3) two species showed significant positive associations with corymbose