Abstract: By using microsatellite markers, the genetic structure of six domestic duck resources distributed in Middle China, including Huainan Sheldrake, Youxian Sheldrake, Linwu, Jingjiang Sheldrake, Mianyang Sheldrake and Enshi Sheldrake, was analyzed in this experiment. The results showed that the mean heterozygosity of six duck populations was 0.580 1, the highest of which was Jingjiang Sheldrake (0.551 2), and the lowest was Youxian Sheldrake (0.603 5). The value of heterozygosity reflected the rich diversity of those populations. And considerable population differentiation was observed by F-statistics analysis and 22.5% of the total genetic variation came from population differences, this result firmly affirmed each breed was of its own genetic diversity. The DA genetic distances suggested the longer differentiation existed among those breeds. Based on the distances among those populations, the results of NJ clustering were formed, the first group was Jingjiang Sheldrake, Mianyang Sheldrake and Enshi Sheldrake; the second group was Youxian Sheldrake and Linwu; the third group was Huainan Sheldrake. In terms of the results, those could provide not only basic molecular data for the research on the characteristics of local breeds in Middle China but also scientific basis for the conservation and utilization of those breeds.