Japanese field vole (Microtus montebelli ) is an endemic species of Japan, and distributed in Honshu, Kyushu and Sado Island. The vole inhabits farmlands, dry riverbeds and grass fields both elevations. Grassland accounts for less than 1% of the land area and is widely scattered across Japan. In this study, we aimed to understand the genetic structure and the history of dispersal and fragmentation of current populations and now this relates to past climate change. We captured 196 voles in 22 sites, and analyzed mitochondrial cytochrome b sequences and seven nuclear polymorphic microsatellite loci. Genetic diversity was generally high in populations of northern Japan and decreased toward southern Japan. The Bayesian phylogenetic analysis from cytochrome b sequences data revealed two lineages in Kyushu region and five lineages in Honshu region. On the other hand, the model-based clustering analysis STRUCTURE from microsatellite data revealed three lineages in Kyushu region and admixture of several lineages in Honshu region. We discuss the formation of these patterns in mitochondrial and microsatellite data, with consideration of range dynamics in relation to environmental fluctuation and dispersal ability of the vole.