Taxonomic analysis has previously revealed that the species of moles that inhabit Japan are characterized by exceptional species richness and a high level of endemism. Here, we focused on the evolutionary history of the four Japanese mole species of the genera Euroscapter and Mogera, examining mitochondrial cytochrome b (cyt b) gene sequences and comparing them with those of continental Mogera wogura (Korean and Russian populations), M. insularis from Taiwan, and Talpa europaea and T. altaica from the western and central Eurasian continent, respectively. Our data support the idea that in a radiation center somewhere on the Eurasian continent, a parental stock evolved to modern mole-like morph and radiated several times intermittently during the course of the evolution, spreading its branches to other peripheral geographic domains at each stage of the radiation. Under this hypothesis, the four lineages of Japanese mole species, E. mizura, M. tokudae, M. imaizumii, and M. wogura, could be explained to have immigrated to Japan in this order. Mogera wogura and M. imaizumii showed substantial amounts of geographic variation and somewhat complicated distributions of the cyt b gene types. These intraspecific variations are likely to be associated with the expansion processes of moles in the Japanese Islands during the Pleistocene glacial ages.