The Rocky Mountain Red Fox (Vulpes vulpes macroura), once common in the Blue Mountains ecoregion of northeastern Oregon, was considered rare in eastern Oregon by the 1930s and thought to be extirpated by the 1960s, when putatively new Red Fox populations began to appear. Although the new foxes were long presumed to be nonnative (originating from fur-farms or deliberate release), they were often phenotypically similar to native Red Foxes, suggesting the alternative possibility that they arose from range expansions, either by small numbers of remnant native foxes at higher elevations or by Rocky Mountain Red Foxes to the east. In this study, we used mitochondrial DNA to investigate the origins of extant Red Fox populations in northeastern Oregon. Our findings show that both native and nonnative sources contributed to the Red Fox populations currently occupying this region. In particular, Red Foxes in montane habitats of their former range in northeastern Oregon reflect predominantly native ancestry, whereas those in more lowland habitats outside the boundaries of their former range represent a mix of native and nonnative ancestry. Recognizing the existence of foxes with native ancestry in northeastern Oregon may shape management decisions regarding this species, especially in respect to control versus conservation.