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The Shasta salamander, Hydromantes shastae, is a geographically restricted lungless salamander (Plethodontidae) exhibiting remarkable evolutionary diversification at small spatial scales. Tissue samples were sequenced for the mitochondrial cytochrome b and 16S genes. Bayesian phylogenetic analyses revealed five statistically supported clades with large divergences between lineages. In three different pairwise comparisons showing high levels of genetic differentiation, neighboring samples located a minimum of 3.5 km apart were at least 4.5% divergent in the cytochrome b gene. Allozyme data were analyzed using multidimensional scaling and population structure software. With relatively high values of Nei's genetic distance and low levels of gene flow for 18 allozyme loci, these nuclear data support the hypothesis that significant isolation and diversification at small spatial scales warrants recognition of additional species. Morphometric analysis finds three groups, in agreement with analyses of molecular data. The combined concordant results from analyses of mitochondrial genes and nuclear markers show the Hydromantes shastae complex to be highly structured across its restricted range. Accordingly, H. shastae is rediagnosed and restricted to the eastern portion of its former range, and two new allopatric species are named.