Background: Contemporary climate change is affecting nearly all biomes, causing shifts in animal distributions, phenology, and persistence. Favorable microclimates may buffer organisms against rapid changes in climate, thereby allowing time for populations to adapt. The degree to which microclimates facilitate the local persistence of climate-sensitive species, however, is largely an open question. We addressed the importance of microrefuges in mammalian thermal specialists, using the American pika (Ochotona princeps) as a model organism. Pikas are sensitive to ambient temperatures, and are active year-round in the alpine where conditions are highly variable. We tested four hypotheses about the relationship between microrefuges and pika occurrence: 1) Local-habitat Hypothesis (local-habitat conditions are paramount, regardless of microrefuge); 2) Surface-temperature Hypothesis (surrounding temperatures, unmoderated by microrefuge, best predict occurrence); 3) Interstitial-temperature Hypothesis (temperatures within microrefuges best predict occurrence), and 4) Microrefuge Hypothesis (the degree to which microrefuges moderate the surrounding temperature facilitates occurrence, regardless of other habitat characteristics). We examined pika occurrence at 146 sites across an elevational gradient. We quantified pika presence, physiographic habitat characteristics and forage availability at each site, and deployed paired temperature loggers at a subset of sites to measure surface and subterranean temperatures. Results: We found strong support for the Microrefuge Hypothesis. Pikas were more likely to occur at sites where the subsurface environment substantially moderated surface temperatures, especially during the warm season. Microrefugium was the strongest predictor of pika occurrence, independent of other critical habitat characteristics, such as forage availability. Conclusions: By modulating surface temperatures, microrefuges may strongly influence where temperature-limited animals persist in rapidly warming environments. As climate change continues to manifest, efforts to understand the changing dynamics of animal-habitat relationships will be enhanced by considering the quality of microrefuges.