Using karyotypic, morphological, and molecular data, we compared Hynobius yunanicus with a sympatric species, Pachyhynobius shangchengensis. Similar to P. shangchengensis, H. yunanicus has a diploid chromosome number of 64, with five large pairs, six medium pairs, and 21 microchromosome pairs. In both H. yunanicus and P. shangchengensis, the vomerine teeth are arranged in two arched series, the lacrimals do not reach the orbits but are in touch with the external nares, and a gap between the pterygoid and maxillary is always present. The two species not only clustered together on a phylogenetic tree based on mitochondrial DNA sequence data but also share an identical haplotype. Therefore, H. yunanicus is not a valid species but a synonym of P. shangchengensis.