Abstract: The fungal microbiota of rice wine samples,which collected from Enshi Hubei province,were revealed by MiSeq high throughput sequencing technologies. The results showed that Ascomycota,Mucoromycotina,Basidiomycota,Chytridiomycota and Blastocladiomycota were the main fungal phyla. At the genus level,Saccharomycopsis,Rhizopus and Amylomyces were the core dominant fungal genus,with average relative abundance of 62.44%,20.28% and 4.42%,respectively. Meanwhile,10627 OTUs were clustered with 97% similarity and OTU2793、OTU8553、OTU2342、OTU4367、OTU9019、OTU4274 and OTU5981 were shared by all samples with the cumulative average relative abundance of 80.64%.In addition to a large number of common fungal communities,the samples also contain unique fungal groups. It was also worth mentioning that 10 samples could be divided into two clusters based on fugal microflora,and the difference of fungal community structure in cluster Ⅰ was significantly higher than that in cluster Ⅱ(p<0.05). The result of Mann-Whitney test showed that Saccharomycopsis,Rhizopus,Amylomyces and Poitrasiawere identified as key fungal groups caused significant differences in the two microbial community structures of rice wine samples.