The “blind mouse” genus, Typhlomys, is an ancient taxon in the family Platacanthomyidae, comprising 2 living species and 4 living subspecies. We sequenced 3 mitochondrial (CytB, COI, and ND₂) and 2 nuclear (GHR and IRBP) gene segments to estimate the phylogenetic relationships of the species and subspecies, and to delimit species boundaries. We also evaluated patterns of morphological and morphometric variation of the skull. The molecular results suggest at least 5 species are present, corresponding to the 2 recognized species (Typhlomys cinereus and T. chapensis), 1 species previously considered a subspecies (T. ci. daloushanensis), 1 new species (Typhlomys nanus sp. nov.), and 1 putative new species, for which we lack adequate morphological specimens. We also determined that the subspecies Typhlomys cinereus jingdongensis is conspecific with T. chapensis. Diversification of the genus occurred in the late Miocene and Pliocene. The new species, T. nanus, is distributed in eastern and northeastern Yunnan at middle to high elevations (2,000 m to > 3,000 m above sea level). Interestingly, we detected a frameshift mutation within the IRBP gene, which is the 1st molecular evidence for the degradation of vision.