It has been suggested based on morphological data that a distinct form of Clethrionomys rufocanus (Sundevall 1846) inhabits Daikoku Island, Hokkaido, Japan. This has been treated by some researchers as a different species and has thus, created confusion as to what its real taxonomic status is. Aside from this, it has been suggested that another species of vole exists in the island. We thus compared the genetic and morphological variation of the voles from Daikoku Island with populations from its nearby mainland, Akkeshi and Shibecha and with the two other related species, C. rutilus and C. rex. Direct sequencing of the partial mtDNA control region (745-bp) in 81 voles from the three populations revealed 27 haplotypes. A single unique haplotype was observed in Daikoku, 10 were identified in Akkeshi, and 18 were from Shibecha. Examination of the diagnostic upper third molar pattern indicated that all specimens collected in the island were C. rufocanus. However, discriminant function analysis of the cranial measurements of voles from Daikoku and the mainland (Akkeshi and Shibecha) indicated morphological differentiation. Our genetic and morphological results confirm that a single vole species, C. rufocanus, is present in Daikoku Island, which relatively recently originated from mainland Hokkaido.