First data on morphological and mitochondrial variation in the long-tailed hamster Cricetulus longicaudatus is presented. In contrast to genetically monomorphic populations of Mongolia and Tuva, the northeastern part of the Qinghai-Tibetian Plateau was found to harbor several divergent mtDNA lineages. This pattern suggests a recent expansion of the long-tailed hamster to the northern part of its recent range, which started from Tibet, presumably, in the late Middle Pleistocene. Several populations from the northern edge of the species range were found to be morphologically but not genetically distinct. The apparent disagreement between genetic and morphological data can be explained by rapid morphological evolution in peripheral isolates.