Genomic approaches can be used to discriminate recent inbreeding from longer-term processes influencing genetic diversity, which can inform the risk of inbreeding depression. Native red foxes in the contiguous western United States declined in the early 1900s and remain scarce in the Pacific mountains. In 2021, the Sierra Nevada population of the Sierra Nevada subspecies (Vulpes vulpes necator) was listed as federally endangered, with inbreeding depression a primary threat. Previous studies suggest that other Pacific mountain populations (V. v. necator in the southern Cascades, V. v. cascadensis in the northern Cascades) also have reduced genetic diversity. Here we used whole-genome sequences to investigate the risk of inbreeding depression in 27 individuals sampled from four high-elevation populations in the Pacific mountains and, for reference, 6 individuals from closely related populations with greater connectivity. We found that despite high levels of genome-wide diversity, all Pacific populations have experienced recent inbreeding, with the greatest intensity in the southern Cascades of California. We also compared genetic load among populations and, within the California Cascades, before and after a rare immigration event. Our findings inform the management of Pacific mountain red foxes and highlight the utility of genomic approaches in conservation of small populations.