The Queen Charlotte Islands (QCI), British Columbia, have many putative endemic avian subspecies. We evaluated four species—Northern Saw-whet Owl (Aegolius acadicus), Hairy Woodpecker (Picoides villosus), Steller's Jay (Cyanocitta stelleri), and Pine Grosbeak (Pinicola enucleator), each with a phenotypically described endemic subspecies from QCI—for uniqueness, conservation concern, and management. The Chestnut-backed Chickadee (Poecile rufescens), with no endemic subspecies from QCI, was included for comparison. We hypothesized that the four endemics would have similar phylogeographic patterns of genetic divergence and coalescence between QCI and possible source populations, because they may share a glacial-refugium history. Cytochrome b was sequenced for all species from Alaska, Washington, and QCI. The four species with endemic phenotypes from QCI had significant genetic divergence from nearby conspecific populations, though variation in divergence times indicated varying colonization histories. Given the corroboration between morphological and genetic evidence for derived populations from QCI, the four endemic subspecies exhibit hallmarks of being evolutionarily significant units (ESUs) and, at the least, should be considered separate management units (MUs), distinct population segments (DPSs), or designatable units (DUs). This is reflected in existing subspecific nomenclature, which our genetic results support. Chestnut-backed Chickadees had genetic differentiation in southeast Alaska as a separate MU but no significant differentiation in QCI. Our results indicate that QCI has been an important area for the generation of avian diversity below the species level and that it is an important area for the conservation and management of birds in northwestern North America.