ABSTRACT: The migratory histories of the endangered freshwater goby Rhinogobius sp. BI (Bonin Island type) collected from 6 stations on Chichijima Island, part of the Bonin Islands chain in Japan, were studied by examining the environmental signatures of strontium and calcium concentrations in otoliths using electron probe microanalyses. The Sr:Ca ratios in the otoliths showed when the gobies had experienced various salinity environments such as freshwater, brackish water, and seawater. The otolith Sr:Ca ratios of almost all Rhinogobius sp. BI from rivers connected to the sea reflected the typical amphidromous life history. In contrast, fish collected upriver from a dam, disconnected from the downstream area, utilized freshwater habitats only, reflecting an artificially landlocked life history. Further flexible migration patterns were found in fish from areas downstream of the aforementioned dam (in a river connected to the sea), indicating that they utilized freshwater, brackish water, and seawater in their larval and adult life period. The present study clearly suggests that the migratory histories of Rhinogobius sp. BI are highly variable within habitats and that they have flexible migratory patterns, allowing them to utilize the full range of salinity during their life history.