Abstract: 9 microsatellite loci were used to detect mean heterozygosity, polymorphism information content(PIC) and genetic relationships in 11 duck populations. The results showed that mean heterozygosity of 11 duck populations was 0.659 9, and mean PIC was 0.596 6. Among the 11 duck populations, mean heterozygosity of the Black Feather Muscovy（white hair）was the highest (0.694 8), and that of Jingjiang Partridge duck was the lowest(0.575 7). There were similar results in PIC. The 11 duck populations were divided into three group by NJ phylogenetic tree based on the genetic distance. The first group included White Feather Muscovy duck, Black Feather Muscovy duck, Black Feather Muscovy duck（white hair）;the second group included Shan Partridge duck, Jinding duck, Gaoyou duck; and the third group included Sumu White duck, Sumu Black duck, Longbai duck, Sumu Partridge duck, Jingjiang Partridge duck.