Alpine and arctic environments are thought to be more vulnerable to climate change than other lower-elevation and lower-latitude regions. Being both arctic and alpine distributed, the Alaska marmot (Marmota broweri) is uniquely suited to serve as a harbinger of the effects of climate change, yet it is the least-studied marmot species in North America. We investigated the phylogeography and genetic diversity of M. broweri throughout its known distribution in northern Alaska using the mitochondrial cytochrome b gene to better understand how post-Pleistocene changes and population fragmentation have structured genetic diversity. Our results show significant, although shallow, geographic structure among Alaska marmot populations. The diversity within and among populations is consistent with 2 phylogeographic hypotheses: Alaska marmots persisted in the eastern Brooks Range, Ray Mountains, and Kokrines Hills during the Pleistocene and have only recently expanded into the western Brooks Range; and the western Brooks Range served as a refugium as well and those populations have undergone a bottleneck resulting in reduced genetic variation in extant populations. Levels of mitochondrial deoxyribonucleic acid diversity are lower in M. broweri than in any other codistributed small mammal species and alpine mammal species with comparable data available. This is the 1st phylogeographic study of any marmot species and provides a baseline measure of the current structure and diversity within M. broweri.