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Aim The evolutionary process of an organism provides valuable data toward an understanding of the Earth evolution history. To investigate the relationship between the uplift of the Qinghai-Tibet Plateau (QTP) and mammalian evolution since the late Cenozoic, the geographic distribution of genetic variations in the Tibetan hamster Cricetulus kamensis was investigated using phylogeographical methods. In particular, population divergence, demographic history, genetic variation, and the prediction of species distribution area were investigated. Location The Qinghai-Tibet Plateau. Methods A total of 53 specimens, representing 13 geographic populations, were collected from the QTP. The phylogeographical pattern and demographic history of C. kamensis were analyzed, and the probable factors in the QTP uplift and the Quaternary glacial periods were inferred from one nuclear and four mitochondrial genes. Furthermore, the species distribution model (SDM) was used to predict changes in potentially suitable habitats since the last Interglacial. Results Phylogenetic analysis demonstrated that two major genetic differentiations of the C. kamensis population occurred during the Early Pleistocene that were influenced by the Qing-Zang tectonic movement from the Middle Pliocene to the Early Pleistocene. Genetic distance between two major clades indicated low genetic divergence. Demographic history analysis showed that the C. kamensis population was affected by the Quaternary glacial period. SDM analysis indicated that C. kamensis was endemic to the QTP and the suitable habitat was affected by climate change, especially during the Last Glacial Maximum (LGM). Main conclusion Our results indicated that the QTP uplift led to the population divergence of C. kamensis, and vicariance well accounted for the geographic distribution of genetic variation in C. kamensis as a result of genetic divergence and lack of gene flow. The genetic distance shows that C. alticola may be a subspecies of C. kamensis. Demographic history analysis suggests that the QTP was affected by the last glacial period. SDM analysis supports that almost the entire QTP is covered by a huge ice sheet during the LGM.