In the face of climate change, populations must either adapt to persist in their current habitats or shift their range to find more ideal habitats. For those that cannot shift their range, investigating the genetic consequences of past climate change can help assess risk of extinction. We employed whole genome resequencing of modern samples and historic museum specimens to understand the American pika’s genetic history over the past century in the Great Basin, Southern Cascades, and Sierra Nevada ecoregions. The American pika serves as an early warning indicator of the detrimental effects of climate change due to their narrow tolerance range, particularly for temperature and water balance. We evaluated genetic diversity and effective population sizes of modern or historical populations at multiple sites and observed decreases in both metrics over the past century. Historic genetic diversity was highest in sites with low temperatures and high precipitation. Our study provides more insight into why populations in some regions are experiencing more extirpation events than others and fills gaps in our knowledge of how climate change affects this species. This study is one of a few to leverage historic and modern genetic data to assess its vulnerability to human-induced climate change.