Abstract: Three rice wine samples were collected from Xuanen county,Enshi Tujia and Miao Autonomous Prefecture,Hubei province and MiSeq high-throughput sequencing technology were established to investigate the biodiversity of bacteria and fungi of them. The result indicated that Pediococcus,Bacillus and Lactobacillus affiliated to Firmicutes,Pseudomonas,Acinetobacter and Enterobacter affiliated to Proteobacteria were domain generas,with the relative abundance of 74.10%,6.32%,3.03%,3.58%,1.22% and 1.08%,respectively. The result also indicated that Wickerhamomyces,Saccharomycopsis and Trichomonascus affiliated to Ascomycota,Amylomyces affiliated to Mucoromycotina were domain generas,with the relative abundance of 44.67%,23.10%,1.20% and 27.06%,respectively. The sequences cluster to core bacterial and fungal OTU were 89.88% and 98.80% of total sequences. Thus,rice wine samples collected from Xuanen county shared a large number of core bacterial and fungal microbiome.