ABSTRACT Alpine species are inordinately threatened by habitat loss and precipitation changes resulting from climate change. In North America's Pacific Northwest (PNW), three closely related alpine mammal species—hoary, Olympic, and Vancouver Island marmots—may face greater negative impacts of climate change relative to species found at lower elevations. Phylogenetic studies have found these three species form a monophyletic complex; however, discordant evolutionary histories between mitochondrial and nuclear genes suggest that gene flow may have occurred between these marmot species. Furthermore, mitochondrial data find two reciprocally monophyletic mitochondrial clades (haploclades) of hoary marmots. Nuclear data do not recover this pattern, and interspecific relationships among the markers are not consistent. We used nine microsatellite loci and ultraconserved elements (UCEs) to explore patterns of nuclear gene flow among marmot species in the PNW. Analyses of microsatellite data indicate no current gene flow between hoary and Vancouver Island marmots or between hoary and Olympic marmots but do reveal nuclear gene flow among hoary marmot haploclades. Additionally, UCE data reveal historic gene flow between hoary and Vancouver Island marmots. Overall, our results suggest that historic mitochondrial introgression between hoary and Vancouver Island marmots, as well as male‐biased dispersal, are driving mito‐nuclear discordance in this species complex.