The American pika (Ochotona princeps) is a small, herbivorous mammal native to western North America. While there have been recent population declines across the species range, population trajectories vary considerably. Within the Sierra Nevada (SN) subspecies (O. p. schisticeps), Great Basin (GB) populations have experienced declines at a much faster rate than populations in the SN mountain range. Differences in habitat quality between the ecoregions likely plays an important role in this difference. Various factors shape habitat quality. In this study we characterize diet as one proxy for habitat quality. GB populations are declining more quickly, therefore we hypothesized that habitat quality would be lower in the GB as compared to the SN populations. Specifically, we predicted that the SN samples would have greater taxonomic diversity and higher nutritional value. We used a DNA metabarcoding approach to characterize diets of pika populations throughout California and Nevada. We analyzed 384 pika fecal samples and identified more than 90 plant genera. There was no significant difference between the SN and GB pika diets in terms of taxonomic diversity. However, diet composition was distinct with few genera shared between the regions. Analysis of whether diets vary in terms of nutritional quality is ongoing.