The Humboldt (Spheniscus humboldti) and Magellanic (S. magellanicus) Penguins overlap over 1100 km along the coast of the southeastern Pacific Ocean, and much has been hypothesized about hybridization between them. We visited Puñihuil and Metalqui islands, southern Chile (41–42° S), where both species form mixed colonies; these are also the Humboldt Penguin's southernmost colonies. We observed one mixed pair attending chicks and two adults of intermediate color pattern, one of which tended a chick at a nest. Additionally, on the basis of analysis of 30 blood samples of Humboldt Penguins from the Puñihuil colony, we report the first documented Humboldt × Magellanic Penguin hybrid. Judged from the pattern of restriction fragments, this bird had a Magellanic dam and a Humboldt sire. We sequenced mitochondrial and nuclear copies independently to confirm these results. We suggest that hybridization at Metalqui and Puñihuil is encouraged by the low abundance of the Humboldt Penguin rather than by failed mate recognition.