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Tailed frogs are distributed in high‐gradient streams within the disjunct mesic forests of the Pacific North‐west and represent the basal lineage of the anurans. We sequenced 1530 nucleotides of the mitochondrial cytochrome b and NADH dehydrogenase subunit two genes from 23 populations and used parsimony, maximum‐likelihood, and nested‐clade analyses to estimate relationships among populations and infer evolutionary processes. We found two divergent haplotype clades corresponding with in land Rocky Mountain populations and coastal populations and separated by up to 0.133 substitutions per site. Within the coastal assemblage, haplotypes formed clades by mountain range with 0.010‐0.024 substitutions per site divergence among populations. Inland haplotypes exhibited minimal genetic structure, with the exception of 0.021 substitutions per site distance between populations from the East Fork …