Abstract: In order to detect the polymorphism of MC1R gene and analyze the distribution of polymorphism in domestic duck, white Muscovy and mule duck, 769 individuals of 8 duck populations were studied for searching single nucleotide polymorphism (SNP) by PCR direct sequencing. The results showed there had a synonymy mutation at A399G in MC1R gene, which could be restricted by Hin61 enzyme. Then, the polymorphism of the restriction enzyme site was detected by using PCR-RFLP. The results showed that two genotypes AG and GG were detected in individuals with white plumage, while only genotype AG was detected in those with black plumage in mule duck. Only GG genotype was found in the Putian black duck and the female parent of white feather mule duck. There was no significant association between the polymorphism of MC1R gene and the plumage color of duck was discovered. There was no polymorphism in domestic duck and white muscovy duck. Only AA genotype was found in white muscovy duck and GG genotype was found in domestic duck. The genotype AG was found in most individuals of mule duck and GG genotype in a few of individuals. The genotypes distribution at A399G mutation site were significantly different (P＜0.01) among the three duck breeds by chi- square Test. The research provides a new method for identification and distinguishing domestic duck, white muscovy duck, mule duck, and conservation of Muscovy duck.