The estuarine hermit crab, Clibanarius ambonensis is reported from Iriomote Island, southern Ryukyu Islands, Japan. This is the first record of the species from outside Indonesian territory. Clibanarius ambonensis was found on prop roots or trunks of Rhizophora stylosa or on rocks adjacent to the trees, which were exposed to the air at low tide time. The habitat seems to distinguish C. ambonensis in the field from the other local congeners inhabiting estuarine and mangrove areas such as C. longitarsus and C. striolatus. The latter two species usually inhabit the sand or mud surface of the estuarine and mangrove areas.