During the production process of this beverage, Chinese starter culture and wheat Qu (Chinese koji) are used. The microbiota of rice wine was identified by DGGE and some microorganisms were found, such as: Lactobacillus, Staphylococcus, Saccharopolyspora, Buttiauxella, uncultured microorganisms, and some microorganisms belonging to the Enterobacteriaceae family (Luan etal.,2013). In addition to microorganisms found by DGGE, Enterobacter, Pantoea, Pseudomonas, Propionibacterium, Acinetobacter, Burkholderia, Streptococcus, Weisella, Leuconostoc, and Lactococcus were found in other study of microbiota of rice wine. However, Enterobacter and Pantoea were related with most of reads and these bacteria can cause opportunistic infections in some hosts (Fang etal.,2015). The microbial community in Shaoxing rice wine was characterized by Illumina-based sequencing using Illumina Hiseq2000, for the purpose of understanding better, the microbial ecology during the fermentation process of this beverage. In this study, from 21 to 23 million reads were generated by Illumina-based sequencing and Bacillus sp., Staphylococcus sp., Sacharopolyspora sp., Streptomyces sp., Mycobacterium sp., Rhodococcus sp., Frankia sp. and other were identified in the 5days, while those identified at 30days, were Lactobacillus sp., Pantoea sp., Arthrobacter sp., Kocuria sp., and others, too. However, some unculturable microorganisms were not identified.