We make an attempt to solve the low reproductive rate problems came from the wild bar-headed geese domestication by 16S rRNA gene sequencing. Our results characterize the first molecular examination of the microbial communities within the bar-headed goose GI tract, and provides evidence that qualitative differences exist in different breeding pattern groups (wild, semi-artificial breeding and artificial breeding). Biomarkers at phylum, class, order, family, and genus level for different groups were analyzed.