Given the increase in anthropogenic influences, decreased genetic connectivity of wildlife populations is particularly important for management planning as it can threaten genetic diversity by reducing effective population size. Increased population genomics resolution with the advances of high throughput sequencing has allowed conservation biologist to assess previously unresolvable questions. For example, wolves in the Pacific Northwest USA (PNW) have recently re-established through colonization either from reintroduced inland US populations or from a unique ecotype found in coastal British Columbia (cBC; Canada). If the PNW wolves are contiguous with the inland populations, less protection may be deemed necessary; however, if genetic connectivity between PNW and cBC populations exists, different protection measures may be recommended. To assess the genetic source of PNW wolf populations, we generated data from a capture array and found that PNW wolves have multiple genetic sources and have varying degrees of admixture across geographic space. Additionally, we used ecological niche modeling to assign each pack’s probability of presence in inland or coastal habitat. We found that two western PNW packs are more likely to exist in coastal habitat. Continued migration from cBC to PNW will contribute genetic diversity and possibly decrease inbreeding in the re-established PNW population. Our sequence capture array also targeted putative loci under selection, giving us insight into gene flow patterns for functional genetic variation potentially linked to local adaptation in these populations. These findings need to be considered when designing accurate conservation and management plans for wolves naturally re-colonizing the PNW.