To investigate the species composition and genetic characteristics of Far Eastern daces, genus Tribolodon, in the Tama River, Japan, partial DNA sequences of the mitochondrial DNA control region were compared among specimens from the whole river system. Specimens of Tribolodon hakonensis (n = 257) and Tribolodon brandtii maruta (n = 193) were examined in this study. Inconsistencies in species identification according to genetic and species-specific morphological traits, i.e., breeding color and cephalic lateral line system, were found between some sympatrically distributed specimens (17/450; 3.8%), indicating possible hybridization between T. hakonensis and T. brandtii maruta. The two species were sympatrically distributed in the lower reaches, whereas T. hakonensis solely appeared in the upper reaches and headwaters. In T. hakonensis, we found obvious genetic divergence between the lower and upper reaches, suggesting reproductive isolation related to alternative migration patterns of anadromous and river-resident forms, respectively. Further, it is suggested that native and introduced T. hakonensis populations coexist in the lower reaches and headwaters, whereas the former solely inhabit, or are dominant, in the upper reaches.