Abstract: The genetic polymorphism of five duck breeds was detected by eight microsatellite markers.Genetic heterozygosity,polymorphic information content and genetic distance were calculated by allele frequency,and the cluster analysis was based on genetic distance.The result showed that the average effective allele number per locus was 2.888 at eight microsatellite locus,the average genetic heterozygosity was 0.592~0.658,and the average polymorphic information content was 0.422~0.598 in the five duck populations.The genetic distance was 0.187~ 0.445among the female parents,and the genetic distance was 0.322~0.445 between muscovy duck and the four female parents.The cluster analysis result showed that medium-sized female parent with mini-sized and large-sized clustered together firstly,and then clustered with M18 female parent,finally clustered with Muscovy duck.