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In local reef fish communities, species richness increases with increasing reef area. At Ishigaki Island, Japan, species richness is much lower on large reefs in the shallow back reef than that expected from random placement model simulations (RPMS). As three aggressive territorial herbivorous damselfish, Stegastes nigricans, Stegastes lividus and Hemiglyphidodon plagiometopon, coexist only on such large reefs, we focused on these species and examined patterns of their distribution and abundance on 84 patch reefs of various sizes (area and height). We also examined their aggressive intra- and interspecific behavioural interactions and habitat use on the two large reefs (the largest complex patch reef and the large flat patch reef) among the 84 patch reefs. While the abundance of both S. lividus and H. plagiometopon was highly correlated with patch reef area, that of S. nigricans was closely correlated with patch reef height. For S. nigricans and S. lividus, interspecific interactions occurred significantly more frequently than intraspecific interactions on the large flat patch reef. However, there was no significant difference in frequencies of the two interaction types on the largest complex patch reef, where they three-dimensionally segregated conspecific territories. This study suggested that reef height as well as reef area influence the distribution and abundance of these territorial herbivorous damselfish in the shallow back reef. As large patch reefs cannot be tall allometrically in shallow back reefs, relatively flat patch reefs may not have the high species richness expected from RPMS based on reef area.