We assess variation in mitochondrial DNA (mtDNA) using partial sequences (560 bp) of the COI gene among populations of Japanese land snails, Euhadra peliomphala. Phylogeographical analysis reveals five primary clades that correspond basically to five discrete areas: the Boso Peninsula (B), the Kanto area (K), around Lake Ashinoko (A), the Northern Izu Peninsula (N), and the Southern Izu Peninsula (S). Although there are no current geographical barriers separating these five subpopulations, the borders between each area correspond to palaeogeographical events during the Pleistocene, such as volcanic activities and the disappearance of the landbridge between the Southern Boso area and the mainland of Japan. In addition, our analysis of isolation-by-distance and the distribution of pairwise sequence differences indicate that haplotypes of the B and K lineages have recently increased their population size exponentially. We have also discovered interspecific mtDNA introgression between E. peliomphala and the parapatric species E. brandtii at the contact zone in the Northern Kanto area. Unexpectedly, the E. brandtii-type mtDNA was also found in the populations of E. peliomphala in the Southern Boso area. Because recent contact between both species is unlikely, the introgressed mtDNA of E. brandtii could be a remnant of past hybridization, when E. peliomphala colonized this area via the landbridge that existed in the early Pleistocene.