Abstract: Twenty four Chinese native duck breeds were studied to estimate genetic diversity and genetic structure using microsatellite markers. The genetic relationships between breeds were analyzed in combination with their geographic distribution. A total of 28 microsatellite markers were amplified .All breeds exhibited genetic diversity, through the estimation of polymorphic information content (PIC) and mean heterozygosity (H) index. The mean genetic diversity of the populations was 0.569, while the PIC values for Chinese native duck breeds showed a relatively high level, except APL23 and APL79 were similar (0.414) and of medium polymorphic. The Neighbor-joining was used to calculate the genetic distances. Cluster analysis divided the twenty-four populations into five groups, and the genetic relationships among the populations had obvious association with their phylogenetic relationship with the historical relations and geographical distribution. The development history of native duck breeds in China seemed to have an effect on their genetic structure.