Abstract: In this study,MiSeq high-throughput sequencing technology were used to analyze the bacterial and fungal diversity in 4 rice wine koji samples collected from Jianshi,lacticacid bacterial and yeast strains were also isolated and identified by traditional culture methods. The relative abundances of bacterial genus more than 1.0% were Pseudomonas(40.10%),Pediococcus(14.41%),Weissella(9.62%),Bacillus(5.44%),Enterobacter(3.50%),Pantoea(2.86%),Klebsiella(2.29%)and Lactococcus(2.18%). The relative abundances of fugal genus more than 1.0% were Amylomyces(49.97%),Saccharomycopsis(39.47%)and Wickerhamomyces(3.95%). Ten bacterial and four fungal core operational taxonomic units(OTUs)with relative abundance of more than 1.0% were found in all samples,with the cumulative relative content 61.38% and 93.76%. Ten strains of lacticacid bacteria were isolated and 40% were identified as P. pentosaceus. Meanwhile,10 strains of yeast were isolated and 70% were identified as S.fibuligera. Thus,the Rice Wine Koji in Jianshi area has high microbial diversity.