It is often difficult to determine whether discontinuous distribution resulted from vicariance or dispersals, or how a reportedly introduced species has achieved the present distribution. The hermaphroditic land snails Bradybaena pellucida (BP) and B. similaris (BS) are closely related sibling species to each other. BP is indigenous to western Japan and has been widening its distribution eastward along the Pacific side of Honshu Island. BS is a cosmopolitan species and presumably non-indigenous in Japan. Both species are abundant in suburbs and could be easily dispersed by humans. However, little evidence for this expected history of passive transports has been obtained to explain BP’s discontinuous distribution or BS’s occurrence on most Japanese islands. Our mtDNA sequence analysis showed that BP haplotypes were contrastingly divergent, while Japanese BS haplotypes were too similar to one another for phylogeny. This supports the longer history of indigenous BP and the recent spread of alien BS. Our network analysis indicated that BP and BS have frequently been dispersed by humans. We also found unexpectedly large numbers of base-pair replacements in each species within Japan. This may suggest either their distributions on the islands before human inhabitation or accelerated mutation.