Moving animals on a landscape through translocations and reintroductions is an important management tool used in the recovery of endangered species, particularly for the maintenance of population genetic diversity and structure. Management of imperiled amphibian species rely heavily on translocations and reintroductions, especially for species that have been brought to the brink of extinction by the fungal pathogen, Batrachochytrium dendrobatidis. One striking example of disease-related declines and associated management efforts is in California’s Sequoia and Kings Canyon National Parks with the mountain yellow-legged frog complex (Rana sierrae/muscosa). Limited knowledge of the population genetics of mountain yellow-legged frogs has made long-term conservation planning difficult. To address this, we used 598 archived skin swabs from both extant and extirpated populations across 48 lake basins to generate a robust Illumina-based nuclear amplicon dataset. We found that samples grouped into three main genetic clusters, concordant with watershed boundaries. We also found evidence for historical gene flow across watershed boundaries with a north-to-south axis of migration. Finally, our results indicate that genetic diversity is not significantly different between populations with different disease statuses. Our study provides a population genetic framework for leveraging minimally-invasive samples to be used in conservation management of threatened species.