Despite being listed as endangered, substantial morphological and behavioral variation exists within Black-capped Petrel (Pterodroma hasitata) populations. To examine the population genetic structure of the Black-capped Petrel, we amplified Cytochrome Oxidase 1 sequences from museum specimens collected during 1970–1980 off the coast of North Carolina, USA. These sequences revealed a 1.2% fixed genetic difference between dark and light morphs. Individuals with intermediate plumage all grouped phylogenetically with the light morph. Combined with significant differences in body size and phenology, our genetic results suggest breeding isolation of the dark and light morphs. Consistent with other Pterodroma species, our results imply that the Black-capped Petrel may comprise two distinct, reproductively isolated taxa. Further knowledge about the genetic identity of birds at specific nesting colonies will be valuable for geographic delineation of populations.