Although most species of Anseriformes form long-term or seasonal pair-bonds and breed monogamously, some are thought to be polygynous. The Musk Duck (Biziura lobata) is unique among Anseriformes in that it has been suggested to have a lek mating system. Musk Ducks also display extreme size dimorphism and many secondary sexual traits whose functions are not clearly understood. We studied paternity in a resident population of Musk Ducks in order to explore the genetic mating system and to investigate the role of different male secondary sexual traits. We obtained blood samples from seven males, five breeding females and seven ducklings from six broods on Lake Wendouree, Ballarat, Australia, during the 2003 breeding season and used microsatellite markers to assign paternity to ducklings. Two of the seven sampled males fathered all of the ducklings in the five broods for which we could assign paternity. Both of these males were territorial and heavier, had larger lobes and displayed more frequently than the remaining males. They also produced a large amount of musk. Our results provide the first unequivocal genetic demonstration of polygyny occurring in a wild anseriform population. Discovery of polygyny in Musk Ducks corresponds well with previous field studies suggesting that they have a lek mating system. The skewed paternity distribution towards more ornamented and larger males also suggests that these traits may have evolved under sexual selection.