Spatial genetic structure of populations, on the ecological time scale, is thought to be shaped by the balance between genetic drift and gene flow. Different patterns have been identified between nuclear DNA-based (nDNA) and mitochondrial DNA-based (mtDNA) structures in various mammalian species. A mechanism generating the differences, however, has not been elucidated. In this study, we aim to evaluate the effect of sex-biased dispersal on the genetic structure of populations of the Hokkaido vole on the island scale from 10 km to 400 km. To observe empirical patterns, we compared genetic distances for all pairs of local populations using microsatellite loci of nDNA and the control region of mtDNA. Most pairwise genetic distances based on mtDNA were significantly differentiated, whereas most genetic distances based on nDNA were not significantly higher than zero; these proportions were significantly different (Fisher’s exact test, p = 0.0045). These results indicate that nDNA-based structure was larger than mtDNA-based structure. On the basis of simulation analyses with the individual-based model, we will discuss the effect of male-biased dispersal on the observed genetic patterns.