Current classification of the genus Tamiops is mainly based on pelage color pattern that is prone to seasonal variation or convergent adaptation to environmental selection. The arrangement of four species, Tamiops mcclellandii, Tamiops rodolphii, Tamiops swinhoei and Tamiops maritimus, is regarded as tentative due to difficulty in delineating species, especially the latter two species. We constructed multi-locus phylogenies of all four Tamiops species on the basis of paternal (Y-chromosomal SRY and SMCY7), maternal (mitochondrial cytochrome b gene) and biparental (autosomal IRBP, RAG1 and PRKCI) sequences. Maximum likelihood and Bayesian tree-constructing methods resulted in phylogenies with similar topologies. All genetic markers supported diversification of three main lineages: (1) T. mcclellandii; (2) T. rodolphii; (3) T. swinhoei–maritimus complex. On the basis of 24 T. maritimus from five localities and 10 T. swinhoei from four localities, T. swinhoei and T. maritimus were not reciprocally monophyletic. The six populations of the T. swinhoei–maritimus complex were monophyletic in all loci, except for autosomal loci in one T. maritimus population from Tam Dao, Vietnam. Autosomal phylogenies were more similar to Y-chromosomal than to mitochondrial phylogenies. Incongruence between nuclear and mitochondrial phylogenies indicates that either T. maritimus from Taiwan or T. maritimus from Phu Yen, Vietnam probably descended from ancient hybridization. Diversification of the three main Tamiops lineages was estimated to occur 8.8–6.7 million years ago (mya) and may have been affected by rapid uplift of the Himalayan Mountains in the western part of their range. Multiple divergences from 5.8 to 1.7 mya likely led to the formation of modern Tamiops species. All six populations of T. swinhoei–maritimus complex could be regarded as distinct species. Divergence among T. rodolphii populations in mitochondrial DNA was also at the interspecies level. Our analyses highlight the underestimation of species diversity in the genus Tamiops.