The greater long-tailed hamster is primarily distributed in North Korea, Siberia (Russia), and central and northern China, while the Gansu hamster is restricted to southern Gansu Province, China. The genera Tscherskia and Cansumys have each been considered monotypic. The taxonomic status of these two genera has long been debated, and the specific status of T. ningshaanensis has also been contentious. Researchers have variously treated T. ningshaanensis as a subspecies of either T. triton or Can. canus. In this study, we estimated the phylogeny, divergence times, species delimitation, and biogeographical history of T. ningshaanensis by using one mitochondrial (CYT B) and three nuclear loci (GHR, IRBP, and RAG1) and compared the external and skull morphology variations between T. ningshaanensis and T. triton. The results showed that: 1) The genus Cansumys is a distinct genus in Cricetinae; 2) The notion that the genus Tscherskia is a monotypic genus is unsupported, T. ningshaanensis and T. triton were identified within this genus; and 3) The formation of T. ningshaanensis may have been driven by uplift of the Qinling Mountains. We conclude that T. ningshaanensis is a valid species within the subfamily Cricetinae.