At high altitude, rivers may function as barriers for amphibians. We examined 21 populations of Scutiger boulengeri from the Hengduan Mountains with 1038 base pairs of mitochondrial cytochrome b gene sequences. The haplotypes of S. boulengeri formed three clades on the gene tree, and each clade was restricted to one mountain ridge separated by two major river systems, the Yalong River and the Dadu River. The vicariant pattern of the gene tree suggests that these rivers functioned as effective barriers during population differentiation. On the other hand, mountain ridges may have facilitated amphibian movement. Populations within the uninterrupted mountain ranges of clades II and III, revealed little genetic structure. The northern clade I, harboured a substantial amount of genetic variation, which might be the consequence of the rugged terrain and heterogeneous habitat of this area. Furthermore, one outgroup species, Scutiger glandulatus, formed the fourth clade and nested within S. boulengeri, suggesting that S. boulengeri is likely a paraphyletic species or a species complex.