The red foxes (Vulpes vulpes) indigenous to the mountains of the western United States are high-elevation specialists that could face range reduction due to climatic warming, as well as potential encroachment, loss of adaptive alleles, and displacement by introduced nonnative red foxes. We investigated the genetic integrity of the native Rocky Mountain red fox (V. v. macroura) in Colorado through analysis of the composition, distribution, and patterns of gene flow between native and nonnative red fox populations along an elevational gradient. The study area spanned the high plains around Denver in the east to the alpine zone of the Rocky Mountains adjacent to Gunnison and Crested Butte in the west. We used microsatellites and mitochondrial DNA (mtDNA) from Colorado foxes, along with previously published reference data from other native western and nonnative populations, to evaluate the distribution of native versus nonnative ancestry and its relationship to elevation, distance, and landscape type. Nonnative red fox ancestry predominated in Denver and low-lying areas, whereas native ancestry was most prevalent at high elevations. The genetic integrity of foxes at higher elevations (i.e., within the historical native range) was greater in terms of mtDNA than nuclear DNA, consistent with higher male-mediated gene flow. Nonnative admixture was most pronounced in human-altered landscapes. Our findings provide baseline data necessary to monitor future trends of these Rocky Mountain red fox populations and highlight the potential for similar threats to affect genetic integrity of endangered montane red fox subspecies along the Pacific Crest.