Recent reports have suggested that hybridization occurs between Blue-footed (Sula nebouxii) and Peruvian (Sula variegata) Boobies in northern Peru, but none included morphometric or genetic analyses of apparent hybrids. Over three field seasons, morphological measurements and blood samples were taken from four apparent Peruvian x Blue-footed Booby hybrids on Lobos de Tierra Island, and one apparent hybrid on the Lobos de Afuera islands. Feather samples were collected from one representative of each parental species and one hybrid. Morphological variation of apparent male hybrids was compared to 25 male Peruvian Boobies and 140 male Blue-footed Boobies, and variation in 540 base pairs of the mitochondrial control region and 8 microsatellite loci for all hybrids was compared to 141 Peruvian Boobies and 168 Blue-footed Boobies. Molecular sexing indicated that four hybrids were male and one was female. Male hybrid boobies showed weak transgressive segregation, all hybrids possessed Peruvian Booby mitochondrial DNA and microsatellite alleles from each parental species. Hybridization between these species appears rare and restricted to the islands where both species breed, and pre and post-mating barriers appear well established.