The missing-toothed pygmy weasel, Mustela aistoodonnivalis Wu and Kao, 1991, was originally described from Zhouzhi and Zhashui in the Qingling Mountains in Shaanxi province, China. Subsequently it was considered a subspecies of M. nivalis. During a faunal survey of northwest Sichuan, some specimens of M. aistoodonnivalis were collected. Molecular phylogenetic studies showed that M. aistoodonnivalis formed a distinct clade that was sister to M. eriminea based on one mitochondrial gene and six nuclear genes. Morphologically, there was an obvious difference between M. aistoodonnivalis and M. nivalis, especially the lack of the second lower molar. Geometric morphology studies and species delimitation analysis revealed the valid species status of M. aistoodonnivalis. In summary, we confirm that M. aistoodonnivalis is an independent species rather than a subspecies of M. nivalis, and that it is more closely related to Mustela eriminea.