AbstractChinese indigenous goose breeds possess many outstanding characteristics. However, their genetic diversity has been declining for lack of scientific breeding strategies. For better protection and utilization of these geese, we examined the genetic structure of 13 indigenous grey goose breeds using 31 polymorphic microsatellite markers, including 19 separated with AFLP primers through the magnetic beads enrichment method. According to the allele frequencies of 31 microsatellite loci, mean heterozygosity (H), polymorphic information content (PIC) and genetic distances (D_A) were calculated for each breed. Of the 13 goose breeds, the highest mean heterozygosity was in the Shitou breed (0.6727), whereas the lowest was in the Yan (0.4985). A UPGMA dendrogram showed that Fengcheng Grey, Wugang Tong, Xingguo Grey, Shitou, Wu-zong, Yangjiang, Magang, Gang and Yan were grouped together, while Yili comprised a second group, Chan-gle and Youjiang were in a third group, and Yongkang Grey in a fourth. These results could provide more accurate genetic information for goose breeding.