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Microsatellite markers are now been widely used for the detection and description of micropopulation processes occurring in the populations of domestic animals for the effects of various factors of breeding pressure. Microsatellite loci distributed throughout eukaryotic genomes, making them the preferred genetic marker for high resolution genetic mapping. In recent years, rapid advances have been made in the development of molecular genetic maps. High-density linkage maps are now available for many farm animals, such as cattle, pigs, and goats. In contrast, mapping studies in avian species are much less advanced except in the chicken. According to FAO about 70% of ducks are bred in China. This country is a leader in growing ducks. The Shaoxing breed is one of the three major duck breeds in China. Ducks of this breed are characterized by high performance. According to the Bureau of Product Quality, the age of maturity (the beginning of egg laying) in these birds occurs at 130–140 days. The characteristics of the Shaoxing breed include the fact that the peak period of laying eggs lasts from eight to ten months. On average, one duck in 500 days gives from 290 to 310 eggs, which is one of the highest rates for egg breeds. That is why the purpose of our study was the microsatellite analysis of two populations of Shaoxing breed with 9 locuses was conducted. The selection of birds for the study were carried out on a duck farms in Zhejiang Generation Biological Science and Technology Co., Ltd. and Zhuji Guowei Poultry Development Co, Ltd., and at the laboratory of the Jjejiang Academy of Sciences Institute. Samples collection and DNA preparation: Venous blood samples were collected from 480 ducks (240 ducks of population I and 240 ducks of population II of the Shaoxing breeds) of both populations into 3 ml tubes containing EDTA as anticoagulant agent. In total of 9 investigated loci in the Shaoxing breed population, only one locus was monomorphic (SMO10). The number of different alleles (Na) for each polymorphic locus ranged from 2 (SMO12) to 13 (APL79, CMO11) in population I and from 2 (APL78, SMO12) to 7 (APL79) in population II. On average, one locus had 5.889 alleles in population I and 3.889 of alleles in the population II. The effective number of alleles (Nе) was 1.735 in population I and 1.599 in population II. The number of alleles and the expected heterozygosity (Hexp) values can provide important information for the discrimination of individuals and breeds. The index of expected heterozygosity in population I was 0.336 and 0.307 in population II. The information index (I) was 0,702 in population I and 0,576 in population II. For each population was found private alleles, in population I 6 alleles and in population II just 4 alleles. The results show high level of polymorphism of the studied populations of ducks. The obtained results can be used in the creation of new lines of ducks.