The endangered red wolf (Canis rufus) exists today in captive breeding facilities and a small re-introduced population in North Carolina, USA. The remnant eastern wolf (Canis lycaon) is largely restricted to a single population in Algonquin Provincial Park, Canada. The historical ranges of these two taxa were broadly contiguous, suggesting that they could reflect a single ancestral species. Evaluating this hypothesis based on modern genomes is difficult due to 20th century introgression of coyote (Canis latrans) ancestry and a strong bottleneck associated with the founding of the captive red wolf population. Therefore, to assess the genomic ancestry of these eastern forest wolves, we sequenced whole genomes of museum specimens from wolves collected from their historical ranges during 1872–1941, before the eastward expansion of coyotes.. PCAs, clustering assignments, and D-statistics indicated that red wolves historically exhibited lower levels of coyote ancestry and higher genetic affinities with historical and modern eastern wolves than their contemporary counterparts. These preliminary results suggest a need for re-examination of red and eastern wolf relationships, as eastern wolves could harbor an underutilized source of genetic diversity for red wolf conservation and visa versa.