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Fauna of small mammals of southern Gansu have been studied in three key areas: Lianhuashan Nature Reserve, Taizishan Nature Reserve, and the vicinity of Goin Ba and Lang Mu Monastery. All the key areas are associated with different altitudinal belts and, therefore, with different vegetation types. Altogether, 22 species of small mammals have been found. Among them were ten species of the order Eulipotyphla, two species of the order Lagomorpha, and ten species of Rodenta. The habitat distribution and morphometric characteristics of all species found have been analyzed. Molecular diagnostics as based on mitochondrial gene cytochrome b (cytb) and a karyological analysis were also performed. Using these methods, we revealed several new forms of small mammals. The most interesting was the finding of the Chinese dormouse Chaetocauda sichuanensis Wang, 1985. This was only the sixth report of this species, which had not been recorded earlier in Gansu Province. The small mammals were divided into three faunistic groups according to the species distribution patterns. The first group includes species the distributions of which are mainly confined to the south of Gansu and to Sichuan. The species that live in woodlands on both the eastern and southern slopes of the Qinghai-Xizang (Tibet) Plateau were assigned to the second group. The third group includes species with wider ranges, which are not limited to the slopes of the Qinghai-Xizang (Tibet) Plateau.