Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.