The effects of microhabitat diversity and geographical isolation on the structure of oribatid communities were studied in mangrove forests on the Ryukyu Islands of Japan. The study took place at three sites on two islands 470 km apart. Oribatid mites (Oribatida) were extracted from leaves, branches, bark of trunks (0–50, 50–100, and 100–150 cm high) and of knee roots, and from forest-floor soil and littoral algae, each defined as a microhabitat of oribatid mites. At the 0–50 cm height, the species composition of the oribatid communities on the knee-root bark and the bark of trunks of Bruguiera gymnorrhiza differed significantly from that on the other microhabitats. This difference was attributed to tidal flooding of the mangrove forests. Cluster analysis showed that oribatid communities in the same microhabitat at different sites tended to be more similar than those on different microhabitats at the same site. This implies that the species composition of oribatid communities in mangrove forests is more likely to be affected by factors responsible for microhabitat diversity (characterized specifically by the flooded trunks) than by geographical distance between the islands.