Abstract: In this study, six kinds of Huangjiu koji were used as raw materials to study the microbial community structure and diversity of bacteria and fungi by using high-throughput sequencing technique. The results showed that the bacterial community structure and fungal community structure of rice red koji (JQ1) and millet red koji (JQ2) were similar, the bacterial community structure of wheat koji (JQ3), traditional Chinese medicine koji (JQ4) and alcohol medicine (JQ6) were similar, and the fungal community structures of JQ3, JQ4 and sweet koji (JQ5) were similar. At the gate level, Firmicutes was the dominant bacterial phylum of JQ2, JQ3, JQ4 and JQ6. The dominant bacteria of JQ1 and JQ5 were Proteobacteria. The dominant fungal phylum of 6 kinds of koji was Ascomycota. At the genus level, Lactobacillus was the dominant genus of JQ1, Bifidobacterium was the dominant genus of JQ2, uncultured_bacterium_o_Chloroplast was the dominant genus of JQ3 and JQ5, Virgibacillus was only the dominant genus of JQ4, and Staphylococcus was the dominant genus of JQ6. The dominant fungi in JQ1 were Cyberlindnera, Monascus in JQ2, Aspergillus in JQ3 and JQ5, Xeromyces in JQ4 and Rhizopus in JQ6. It was suggested that, the microbial community structure of six kinds of koji were quite different at the gate and genus level, which would provide a theoretical reference for the follow-up screening of red millet Huangjiu koji.