The Altai weasel, Mustela altaica Pallas 1811 (Carnivora: Mustelidae), is widely distributed across open landscapes of central and eastern Asia. The geographical variation in skull morphology and taxonomic composition of this small mustelid remain poorly known. Based on extensive sampling in museum collections, we analyzed morphometric variation in 23 cranial characters of 232 M. altaica specimens from across its entire range. The multivariate analysis (nonmetric multidimensional scaling) revealed a geographical pattern of variation in cranial size and shape. Based on this result, two morphological groups have been comprehensively characterized. Weasels of the first group differ from those of the second in having larger skulls, wider neurocrania, elongated toothrows, and larger carnassial teeth, as well as in sexual size dimorphism. The first group is confined to the southwestern part of the species range (Tien Shan Mountains, Pamir, the Himalayas, and southern Tibet). The second group is widespread from the foothills of Tien Shan in the west to Khingan and Manchuria in the east. The distribution of the two groups of M. altaica is consistent with the “Out-of-Tibet” hypothesis. The first group presumably can be attributed to M. a. temon Hodgson, 1857, whereas the second group can be treated as nominotypical M. a. altaica Pallas, 1811.