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The Sacramento Mountain salamander (Aneides hardii) is a fully terrestrial plethodontid endemic to mountains in south-central New Mexico. This species is of conservation concern but there is scant knowledge regarding the degree of genetic divergence among populations. This informationis vital for developing an appropriate species management strategy. To address this issue, we generated sequence data from the mitochondrial cytochrome b gene and four nuclear loci to explore population demographic history. Cytochrome b data revealed three deeply divergent (2.3-2.8%) mitochondrial lineages corresponding to distinct mountains (Capitan, White, and Sacramento). Divergence dates suggest separation since the early Pleistocene, and signatures of population expansion in the mid to late Pleistocene. Of 25 haplotypes identified, none were shared among mountains, but genetic diversity differed among mitochondrial lineages and suggested different demographic histories within lineages. A single microsatellite locus identified private alleles in each of the three lineages. Other nuclear loci screened were invariant within and among populations, which corresponds to a lower mutation rate compared with mtDNA. Together these results indicate that each mountain population of A. hardii represents a demographically and genetically distinct management unit.