The migratory history of the Rhinogobius sp. OR morphotype “Shimahire” collected from a slower current environment in the Maruyama River, the Ibo River, and the Kako River, Japan, was studied by examining the strontium and calcium concentrations in the otoliths. The otolith Sr:Ca ratios of almost all samples showed consistently low ratios from the core to the edge, reflecting the fact that the organisms had been living in a freshwater environment their entire lives. The ratios of Rhinogobius sp. CB and Rhinogobius flumineus living in the sympatric habitats with the Rhinogobius sp. OR morphotype “Shimahire” in the Kako River showed an amphidromous and fluvial life cycle, respectively. These findings suggest that the Rhinogobius sp. OR morphotype “Shimahire” has a freshwater resident life cycle.