With all the species of the Phalacrocoracidae generally lumped under one genus, the Phalacrocorax, there are some different theories that the Flightless Cormorant is classified into the genus Nannopterum or that all other species are subdivided into genera such as the Hypoleucos, the Leucocarbo, the Stictocarbo, and the Compsohalieus.
科内の全ての種をPhalacrocorax属1属にまとめてしまう事が多いが、その中でガラパゴスコバネウだけはNannopterum属として分ける説や、他の種もHypoleucos属・Leucocarbo属・Stictocarbo属・Compsohalieus属などに細分化する説などがある。