The taxonomic status of petrels from the North East Atlantic has long been a matter of debate. Breeding colonies of petrels occurring on the islands of Madeira, Bugio and Cape Verde were originally thought to be outlying populations of the polytypic species Pterodroma mollis. Subsequent taxonomic treatments have varied considerably in their classification of birds from these islands. The petrel populations on Madeira and Bugio represent some of Europe's rarest breeding birds and their exact species designation, and hence relation to conservation mandates, is a question of considerable importance. In this study we use molecular techniques alongside more traditional taxonomic characters to confirm the existence of two species of the genus Pterodroma in the Archipelago of Madeira. We also discuss identification of these species in the field and the implications for their conservation management.