We investigated geographic variation in skulls of Japanese and Siberian weasels, and compared variability between the two species using multivariate analyses. In the Japanese weasel, some skull shape variables showed variation correlated with some climate variables. Cluster analysis using Mahalanobis distance showed few clustering patterns related with geographic affinity not in concordance with the clustering pattern of mitochondrial DNA sequence which consisted of two main clades: Honshu and Kyushu-Shikoku clades. In the Siberian weasel, multivariate analyses with an emphasis on insular variation revealed that the skull size of insular populations tended to be smaller than that of continental ones, but no geographic and environmental related variation was observed. In accordance with the phylogenetic pattern of mitochondrial DNA sequence, he Taiwan population is morphologically more distinct from Korean and Tsushima populations. Comparison of variability between the two species revealed that the skull morphology of the Japanese weasel is more variable than that of the Siberian weasel. It seems to be related with a genetic variation that is higher in the former species. These complicated patterns of variation in the Japanese weasel may be formed by a mixture of genetic variation related with migration history of the ancestors of this species and their adaptation to various environments of the Japanese archipelago.