Domestication alters lots of phenotypic, neurologic and physiologic traits between domestic animals and their wild ancestors. Domestic ducks were originated from mallards (Anas platyrhynchos) and some documents also showed that spot-billed ducks (Anas zonorhyncha) could also genetically contribute a small part to the domestication. Compared with the two ancestral species, domestic ducks generally present changes in body size and bone morphology, which is supposed to lead to loss of fight in domestic ducks. In the present study, we performed both genomic and transcriptomic analysis to identify candidate genes in order to elucidate the genetic underlying the phenotypic variation.