Using mitochondrial cytochrome b and 16s gene sequences, we examined the genetic diversity of eastern Batrachuperus distributed in China along the eastern slopes of the Tibet Plateau. The group showed a moderate pairwise divergence compared to other salamander groups. The highest cytochrome b divergence is 10.07%. A phylogenetic analysis of the mitochondrial haplotypes revealed several evolutionarily independent lineages, including the Hongya and Pengxian populations of Batrachuperus tibetanus that probably represent undescribed species. The genetic divergence of Batrachuperus is clearly much higher than currently perceived. The distribution patterns of the mitochondrial haplotypes of the northwestern populations indicated that the dispersal or divergence of Batrachuperus might not be confined to river valleys, although all species in the genus are fully aquatic.