American pikas (Ochotona princeps) are thermally sensitive mammals that live in alpine environments. There have been numerous documented local extinctions of pika populations in hotter, drier regions including the Great Basin. Few genetic studies have assessed these at-risk populations. The goal of this project is to fill those gaps by comparing metapopulations in opposite extremes: low elevation Great Basin in northwestern Nevada and high elevation Sequoia Kings Canyon National Parks in the southern Sierra Nevadas of California. Specifically, we are i) quantifying genetic diversity and structure ii) assessing the influence of landscape and climate-related variables on gene flow and population connectivity, and iii) investigating the correlation and covariation among pika diet, intestinal parasites, and population genetic diversity. From May - August 2021, we collected pika fecal samples, plant vouchers, and conducted vegetation surveys across northwestern Nevada and within Sequoia Kings Canyon National Parks. Here, we present the results of the population genetics study. Great Basin populations have lower genetic diversity, are more geographically isolated and genetically distinct than populations in the Sierra Nevadas, indicating greater vulnerability to rapid environmental change. These results are critical to our understanding of the threats to pika populations and will directly inform conservation and management decisions.