We conducted a comprehensive allozymic analysis of 393 specimens of the Japanese clawed salamander, Onychodactylus japonicus, from 33 populations of northeastern Honshu, Japan. As a result, these populations exhibited extensive geographic genetic differentiation, and four major genetic groups (N-Tohoku, S-Tohoku, Tsukuba, and SW-Honshu groups) were consistently recognized. Of these, the Tsukuba group was geographically isolated from all the others, whereas the N- and S-Tohoku groups, and the S-Tohoku and SW-Honshu groups, respectively, were nearly parapatric, without distinct geographic barriers. The magnitude of genetic distances between the four groups, except for between the N- and S-Tohoku groups, was as large as that normally found among different hynobiid species. A structure analysis detected no admixture of the N- and S-Tohoku groups, whereas few hybrids were found between the S-Tohoku and SW-Honshu around their contact zone. However, genetic exchange between these parapatric groups appeared to be infrequent, suggesting the presence of some isolation mechanisms between them. Within each group, only the S-Tohoku group exhibited an extensive level of population genetic structure that roughly distinguishes the eastern, central, and northwestern subgroups, indicating the complexity of the phylogeographic traits of this group. These results strongly suggest that populations of O. japonicus from northeastern Japan encompass several cryptic species.