Recovery-oriented scientific research is crucial to the conservation and management of imperiled, freshwater species. Alabama Pearlshell, Margaritifera marrianae, is a federally endangered freshwater mussel species endemic to the Murder Creek and Sepulga Rivers in south Alabama. This mussel has been extirpated from over 75 percent of its historical range as a result of anthropogenic habitat deterioration. However, aside from occurrences and host fish relationships, little is known about the species, in particular its molecular ecology. Genetic data are important for management efforts to prevent loss of genetic variation and preserve natural genetic structure. We used a genomic approach (3RAD) to generate molecular data to assess population structure and genetic diversity within the current range of Alabama Pearlshell. Analysis of population genetic structure suggests that gene flow is mostly limited to within drainage systems and is likely restricted by migration of the host fishes. Our findings indicate higher genetic diversity and less inbreeding within populations than expected and conflict with the apparent species decline observed through traditional surveys. Our results are likely representative of high host fish migration, undiscovered portions of the population, or buffering of genetic diversity loss by long generation times. In addition to genomic results, we reviewed current management and restoration efforts for this species and provide suggestions on how best to incorporate genomic results directly into conservation application. Future restoration and propagation efforts should consider the molecular ecology of Alabama Pearlshell and maximize efforts to retain the high genetic diversity found in this study. This project was completed in collaboration with federal, state, and academic partners, including the U.S. Fish and Wildlife Service, the Alabama Department of Conservation and Natural Resources, and Auburn University.