We compared the distribution of migrant bird species between two islands in the Gulf of Maine to examine if differences in habitat resulted in differences in avian species composition and relative abundance during stopover. Ninety-one species were captured on both islands and those species captured on only one island were either breeding species or rare visitors to the islands. Differences in bird species distribution between islands were species-specific and consistent among sampling periods for nearly all species. Twelve species were captured more frequently on Star Island and 11 species more frequently on Appledore Island. Stopover species distribution appeared to be related to habitat structure, vegetation, diet, and habitat area. Scrub-shrub/open habitat breeding species and forest breeding species were not evenly distributed between islands. Island use was most closely associated with breeding habitat. All but two of the eight species that breed in scrub-shrub or open habitat were captured more frequently on Star Island. Ten of the species more common on Appledore Island breed in forested habitat. Nine of the 11 species more common on Appledore Island are area-sensitive in breeding areas, suggesting potential area sensitivity during migration. Differential habitat use indicates a large number of stopover sites in a wide variety of habitats are necessary to meet migration needs of passerine species.