To further understand the population structures of the Japanese badgers (Meles anakuma) on the Japanese islands, we analyzed their bi-parentally inherited microsatellites. Based on genotypes of nine microsatellite loci, the badgers were divided into five discrete clusters: three clusters from the Honshu Island, one from Kyushu and one from Shikoku. We propose that this genetic differentiation among badgers from the Honshu, Shikoku and Kyushu Islands is as a consequence of geographical isolation caused by the Seto Inland Sea. Furthermore, the cluster containing individuals from Shikoku was more differentiated from the other clusters, plausibly attributable to the earlier geological separation of the Shikoku Island from the Honshu and Kyushu Islands. The three clusters in Honshu, however, did not correspond precisely with geographical locations. As indicated in previous studies, based on mitochondrial DNA analysis, the genetic relationships within the Japanese badgers might reflect recent population expansion, occurring over a relatively short evolutionary time-scale. The findings preliminarily indicate that the Japanese badgers do not possess the high levels of philopatry seen in the European badger (Meles meles), a closely related species, although further analyses using balanced sample sizes from a wider range is required.