Abstract: Gene frequency, polymorphism information contents, number of effective alleles and locus heterozygosity were studied in 300 ducks of six populations (Shaoxing duck, Muscovy duck, Cherry duck, Peking duck (Z₁ and Z₄) and Aobaixing duck) using four microsatellite markers (AJ272577，AJ272578，AJ272579 and AJ272580). The result indicated that there are genetic polymorphisms at four microsatellite markers in six duck populations. Four microsatellite markers can be used for genetic diversity evaluation in duck populations. The genetic variability of AJ272578 is the highest, and AJ272579 is the lowest. The genetic variability of Peking duck (Z₁) is the highest, and Aobaixing duck is the lowest in six duck breeds.Based on Nei’s standard genetic distance, dendrograms were constructed using the unweighted pair group method with arithmetic mean (UPGMA)， Shaoxing duck and Muscovy duck were grouped together; Peking duck (Z₁), Aobaixing duck and Peking duck (Z₄) were clustered together, Muscovy duck was clustered another type. Microsatellite genotyping in ducks provided a useful tool for examining the genetic relationships among breeds (populations).