I studied the effect of treehole (microhabitat) size distribution in local habitats on geographic difference in aquatic metazoan community structure by comparing differences between two sites on Iriomote Island, and between Iriomote Island (subtropical) and Tsushima Island (temperate), in southwestern Japan. In treeholes at each local site, the amount of litter, the species richness and total biomass of metazoa were positively correlated with treehole capacity. Between the two sites on Iriomote Island (Shirahama and Komi), the amount of litter, biomass and species number per treehole was greater at Komi where the mean and variance of treehole size were greater, while the dependencies of these parameters on treehole capacity were common to both sites. Total species number was larger at Komi (2 predators and 20 saprophages) than at Shirahama (1 predator and 19 saprophages). Most of the dominant taxa colonized larger treeholes with higher probabilities, although one taxa showed the opposite trend. Treeholes on Tsushima were smaller than those on Iriomote. The metazoan fauna in treeholes consisted of 15 saprophages on Tsushima, being less richer than that on Iriomote Island which had 2 predators and 21 saprophages. However, the dependencies of litter amount and biomass on treehole capacity did not differ significantly between the islands, although treeholes on Iriomote harbored a greater number of species per treehole than those on Tsushima. This study indicated that there are general correlates between community structure within individual treeholes (infracommunity structure) and treehole capacity (microhabitat size). Therefore, microhabitat-size distribution is potentially a significant constraint of local community structure, and its variation may contribute to the variation in local and regional species richness.