Abstract: The genetic diversity and differentiation of twenty six Chinese native goose populations were investigated using 25 microsatellite markers. The total number of animals examined was 1 560. A total of 198 alleles were observed, with mean number 7.92 alleles per locus. Effective alleles number varied from 1.307 0 to 5.795 5, with an average of 3.066 2. The polymorphic information content (PIC) ranged from 0.324 to 0.538, the observed heterozygosity (Ho) ranged from 0.535 1 to 0.754 7, and the expected heterozygosity (He) ranged from 0.383 1 to 0.604 9. As a complete populations, the average Ho , He and PIC were 0.668 6, 0.457 7 and 0.564 0, respectively. Considerable genetic differentiation was observed and 20.7% of the total genetic variation originated from the differences among breeds. The largest Reynolds genetic distance and lowest gene flow were between Youjiang and Yongkang grey geeses, meanwhile, the nearest Reynolds genetic distance and highest gene flow were between Wugangtong and Huoyan geeses. Consensus tree was constructed using the Neighbour-Joining method based on the Reynolds genetic distance, and five groups were found. The results may provide basic molecular data for the research on the germplasm characteristics of native goose breeds in China and scientific basis for the conservation and utilization of those breeds.