Influence of the dams in the Kamo and Nakayama River systems in the Ehime Prefecture on the common freshwater gobies Rhinogobius flumineus (non-diadromous species), R. sp. CB, R. fluviatilis and R. kurodai (amphidromous species) were surveyed using three microsatellite loci. Genetic variability was high in R. sp. CB (0. 900-0. 919) and low in R. flumineus (0.191-0. 278). Considerable genetic differences were observed among the species. The effects of a dam with a reservoir were examined for R. flumineus and R. sp. CB. In R. flumineus (non-diadromous species), genetic differences were not observed between populations above and below the Nakayama-gawa Dam (Nakayama R.). In R. sp. CB (amphidromous species), migratory history was also examined using otolith Sr/Ca ratio. The otolith Sr/Ca ratio analysis confirmed that the population above the Kurose Dam (Kamo R.) was landlocked by the dam. However, genetic heterogeneity was not observed between populations above and below the Kurose Dam.