The spatial patterns of butterflyfish assemblages (Chaetodontidae) were examined within and between five islands of the Ryukyu Archipelago, southern Japan. Despite being the northernmost reef communities in the world and despite the severe natural and human-induced disturbances that have affected them since the 1970s, the coral reefs of the Ryukyu Islands have one of the most diversified assemblages of chaetodontids in the world. A total of 30 species were identified, and species richness per island ranged from 20 to 25 species. On each of the 45 stations prospected, between four and 17 species were recorded, and between 0.75 and 21.75 ind 250 m−2 were counted. Variation in species composition, species richness and abundance between islands was less pronounced than the variation within islands, where assemblages of the major reef environments (i.e. the reef flat, the reef edge, and the reef slope) were distinguished. The highest species richness and abundance were found on the reef slope and the reef edge. Canonical correspondence analysis revealed that depth, substrate complexity, and live coral cover influenced the distribution of chaetodontid fishes. These factors accounted for 20% of the variation in the species data matrix.