California is home to both the native statethreatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F ST = 0.52).