The skull morphology of black bears inhabiting 2 distributional ranges isolated by 2 river basins in northern Japan was compared in order to examine whether the animals represent different populations. We found substantial differences in relative width of the skull and measurements related to the masticatory apparatus, especially in the length of the molar row and palatal width; the former already differs at 1 year of age when the eruption of permanent teeth occurs, suggesting a genetic basis for the difference. Jackknifed classification was able to correctly assign all adult specimens except 1. The results indicate that bears from these 2 areas belong to different populations that might have been isolated for a considerable period, and gene flow between them is limited, even though the distance between the 2 ranges is only several kilometers at the narrowest point. The Japanese black bear might live in small, isolated local populations.