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Daqu provides enzymes and precursors for liquor fermentation, and is the core of liquor fermentation. In this study, 11 strains of Bacillus were isolated from sesame-flavored liquor Daqu, which can not only produce protease and amylase, but also have antagonistic effects on common pathogens Escherichia coli and Staphylococcus aureus. According to the gyrA gene phylogeny analysis, these 11 Bacillus strains belong to three species, B1, Y14, Y15, and YPDW9 belong to Bacillus mojavensis, W7, W13, YPDW6, and YPDW12 belong to Bacillus subtilis, W14, Y5 and YPDW1 belong to Bacillus velezensis. According to the results of random amplified polymorphic DNA (RAPD) typing, these 11 Bacillus strains are completely different. The specific primers were used to randomly amplify the biological control genes expressing lipopeptide antibiotics (bioA, bmyB, ituc, fend, srfAA, srfAB, yngG and yndJ), and they all expressed different expressions in these 11 Bacillus strains. This research provides new ideas for strengthening Daqu and lays a foundation for improving the quality of liquor.