Seventeen microsatellite loci were used to assess the genetic variation and population structure of six endangered duck populations in China. PIC, heterozygosity with two estimators of genetic differentiation （FST and GST）, and Nei＇s standard genetic distance were evaluated. The results showed that these six endangered duck populations showed high polymorphism. The propor- tion of inter-population subdivision among the six duck populations ranged between 17.0 and 14.7%. The average heterozygosity was 0.706, 0.702, 0.691, 0.676, 0.604, and 0.660 in the Gaoyou, Liancheng, Jinding, Beijing, Shaoxing, and Jianchang ducks, respectively. The average PIC ranged from 0.561 to 0.663. Finally, the results showed higher genetic diversity and difference above the levels of genetic variation among all the populations.
