We reinvestigated the phylogeny of all 15 species of Marmota to resolve a conflict between 2 published analyses, one by Kruckenhauser et al. and another by Steppan et al., regarding the Olympic marmot (M. olympus) and to improve resolution in the genus. We acquired fresh samples of M. olympus, combined all available data on mitochondrial DNA (cytochrome b [Cytb] and ND3/ND4), new sequences for ND3/ND4, and 2,000 base pairs (bp) of the nuclear RAG1 gene. All analyses indicate that M. olympus is a much older, rather than more recent, offshoot of the widespread hoary marmot (M. caligata) or Vancouver Island marmot (M. vancouverensis). The mitochondrial data and some RAG1 results are largely congruent, but RAG1 differs on several points, including: the subgenus Marmota appears paraphyletic to Petromarmota, with reciprocally monophyletic Palearctic and Nearctic clades; and the long-tailed marmot (M. caudata) and Menzbier's marmot (M. menzbieri) are not sister species, suggesting mitochondrial introgression. Asia was colonized by Marmota from North America at approximately 4.6 million years ago (mya), followed by rapid diversification of several major lineages. M. olympus diverged from the M. caligata–M. vancouverensis lineage at approximately 2.6 mya, whereas M. vancouverensis and M. caligata diverged at only about 0.4–1.2 mya. M. olympus might have survived in isolation on the Olympic Peninsula in a nunatak refugium throughout a series of glacial maxima.