American pikas (Ochotona princeps) are small, thermally sensitive mammals that primarily live in montane and alpine environments. The Sierra Nevada lineage (O. p. schisticeps) occupies a uniquely broad range of habitats from low-elevation habitat in the Great Basin to more typical pika habitat in the high Sierras. This lineage has experienced numerous local extinctions, most of which occurred in the Great Basin, yet few genetic studies have assessed these at-risk populations. This study aims to fill that gap by conducting fine-scale genetic analyses on populations in low-elevation Great Basin habitat in northwestern Nevada. Here, we use microsatellite genotyping to: (i) quantify genetic diversity and structure among populations within O. p schisticeps, with particular focus on northwestern Nevada; and (ii) assess the influence of primary productivity and climate-related variables on genetic diversity within O. p schisticeps, as well as at the broader species level. Great Basin populations exhibited the lowest levels of genetic diversity. Within O. p. schisticeps, population genetic diversity was positively correlated with annual precipitation—while at the species level temperature explained the most variation in genetic diversity. These results provide insight into climate-driven range contractions predicted for this species and inform conservation and management decisions.