The sound-producing structure in birds is the syrinx, which is usually a two-part organ located at the junction of the bronchi. As each branch of the syrinx produces sound independently, many birds have two acoustic sources. Thirty years ago, we had anatomical, physiological and acoustical evidence of this two-voice phenomenon but no function was known. In songbirds, often these two voices with their respective harmonics are not activated simultaneously but they are obvious in large penguins and generate a beat pattern which varies between individuals. The emperor penguin breeds during the Antarctic winter, incubating and carrying its egg on its feet. Without the topographical cue of a nest, birds identify each other only by vocal means when switching duties during incubation or chick rearing. To test whether the two-voice system contains the identity code, we played back the modified call of their mate to both adults and also the modified call of their parents to chicks. Both the adults and the chicks replied to controls (two voices) but not to modified signals (one voice being experimentally suppressed). Our experiments demonstrate that the beat generated by the interaction of these two fundamental frequencies conveys information about individual identity and also propagates well through obstacles, being robust to sound degradation through the medium of bodies in a penguin colony. The two-voice structure is also clear in the call of other birds such as the king penguin, another non-nesting species, but not in the 14 other nesting penguins. We concluded that the two-voice phenomenon functions as an individual recognition system in species using few if any landmarks to meet. In penguins, this coding process, increasing the call complexity and resisting sound degradation, has evolved in parallel with the loss of territoriality.