Recently, expansion of the number and distribution of sika deer, Cervus nippon, in the Japanese Archipelago has resulted in the disturbance of indigenous gene pools and ecosystems. There are also concerns that the artificial introduction of sika deer to certain areas may aggravate this situation. In order to contribute to the conservation of ecosystems, I examined the current state of genetic disturbance and dispersal routes in the sika deer populations around Toyama Prefecture, one of the main areas of expanding sika deer distribution. Of 12 haplotypes detected by mitochondrial DNA D-loop sequence analysis, 10 were found to belong to a previously detected sika deer group in northern Japan, although the remaining two haplotypes corresponded to the southern Japanese sika deer group. The latter two haplotypes were detected at especially high frequencies in the southern area of Toyama Prefecture, suggesting that these haplotypes may derive from artificially introduced individuals. Occurrence patterns of indigenous haplotypes around Toyama Prefecture revealed immigration into Toyama Prefecture through different routes, mainly in the east and south-west. The genetic results presented here may have application in predicting future dispersal routes, as well as aid in the establishment of effective measures for management of sika deer.