We examined a cranial morphometric data set consisting of 940 specimens, as well as 156 complete sequences of the cytochrome b gene of Eutamias sibiricus. The geographic coordinates of 378 (northern chipmunk: 318; Chinese: 50; Korean: 10) localities were used for distribution modelling. Both morphology and genetics support existence of three subspecies of E. sibiricus: northern E. s. sibiricus, Chinese E. s. senescens, and Korean E. s. barberi. Chinese chipmunks form sister clade to northern chipmunks. Only 5.8% of the specimens have no strong similarities with representatives of their own geographical form in terms of cranial shape; an overwhelming majority of these specimens comes from the region of three taxa distributions junction. We expect two potential contact zones between Chinese and northern subspecies: in the south of the central part of the Great Khingan Range and in the central and south-eastern part of Liaoning, China.