Island populations are at heightened risk of inbreeding due to reduced mating opportunities with unrelated conspecifics. Extensive inbreeding can result in inbreeding depression (reduced fitness of individuals with related parents). Alexander Archipelago wolves (Canis lupus ligoni) are a geographically isolated subspecies that occur in the Southeast Alaskan panhandle, USA and coastal British Columbia, Canada. Wolves on the Prince of Wales Island complex (POW) in Southeast Alaska are expected to have lower levels of resiliency because they are a small, insular population that has experienced habitat fragmentation and cycles of moderate to heavy harvest. To understand the extent of population structure and inbreeding in Alexander Archipelago wolves, we designed a DNA hybridization capture for wolves and sequenced captured DNA from 58 individuals sampled from across Southeast Alaska during 2002–2016. Estimates of the proportion of the genome in runs of homozygosity (F_ROH) regardless of run length revealed that POW wolves were most inbred compared to wolves in other areas of Southeast Alaska. Wolves on POW also had more long (≥10 Mb) runs of homozygosity than the other populations we assessed, indicating more frequent mating between individuals with recent common ancestors (1–10 generations ago). This pattern indicates a smaller population size for POW wolves in the recent past compared to other Southeast Alaskan populations. Wolves on POW exhibit an extent of inbreeding similar to that observed in Isle Royale National Park wolves, a population that has exhibited severe inbreeding depression. Our work demonstrates the utility of using genomic capture data to infer individual inbreeding so that proactive management (e.g. setting population targets and harvest quotas, curtailing habitat alteration, etc.) can be considered to ensure the long-term sustainability of small, isolated populations.