Quaternary environmental change provided opportunities for rapid population expansion; however, the process of building the population spatial structures remains poorly understood. In this study, we determined the mitochondrial cytochrome b and control region sequences of 43 individuals of the large Japanese wood mouse (Apodemus speciosus) from Hokkaido, northern Japan and analyzed these data along with those from 40 other individuals. Consistent with the findings of our previous study, we found that two rapid expansion events, after the last glacial maximum (LGM) and Marine Isotope Stage (MIS) 4, shaped population genetic pattern of A. speciosus in Hokkaido. In northeastern Hokkaido, several ancient lineages that originated during MIS 3 were detected, whereas central Hokkaido was dominated by haplotypes descended from a single lineage that survived the LGM, suggesting that the populations of western part of Hokkaido were newly formed by westward migration from eastern Hokkaido during the post-LGM warm period. Alternatively, as post-LGM vegetation recovery is thought to have occurred gradually from west to east in Hokkaido, population expansion started in the west and moved gradually to the east, resulting in eastward haplotype movement; thus, western and eastern Hokkaido may have served as the haplotype source and sink, respectively.