We examined the population genetics and phylogenetics of Falcipennis canadensis isleibi, a subspecies of Spruce Grouse from the Alexander Archipelago of southeast Alaska, which was recently given subspecies status on the basis of subtle differences in plumage coloration and its limited distribution on several islands. The taxonomic status of Fc. isleibi is particularly consequential, both because little is known about its evolutionary, demographic, and conservation status and because island endemics often face high extinction risks. Samples were collected from central Alaska, British Columbia, and Prince of Wales (POW) and Zarembo (ZAM) islands in the Alexander Archipelago and identified to subspecies using established morphological traits. We sequenced the cytochrome-c oxidase I (COI) subunit of the mitochondrial genome (n = 62) and genotyped each individual at six nuclear microsatellite loci (n = 65). Individuals from POW and ZAM shared a unique mitochondrial haplotype not observed in other populations of other subspecies (F. c. franklinii and F. c. canadensis), whereas haplotypes were shared by individuals identified as franklinii or canadensis. Microsatellite loci revealed significant divergence among all subspecies populations ( = 0.352) as well as divergence between POW and ZAM populations of F. c. isleibi. These data corroborate the morphological classification of F.c. isleibi as a separate subspecies. Spruce Grouse are not managed as a single species by the state of Alaska, but instead as an aggregate with other forest grouse species. Our results indicate that populations of F.c. isleibi warrant special management attention to maintain this distinct evolutionary lineage.