Abstract: To explore the change of bacterial communities of Daqu in different storage rooms, the V3 and V4 regions of bacterial16 S r DNA were analyzed by high-throughput sequencing, the relationship between different Daqu and bacterial diversity was revealed combining the methods of principal co-ordinates analysis and linear discriminant analysis.The groups of A and B were selected in this experiment, according to the tracking data of the department, the mean value of saccharifying power of group A was a half of group B, which indicated obvious difference.The results showed that bacterial community structure was constantly adjusted, Lactococcus and Sebaldella became the dominant genera of group A in the end of storage, while the dominant genera was Bacillus in group B.The bacterial diversity of Daqu had a great difference in group A, in which Thermoctinomyces were the significantly different microbes, while Bacillus were the specific bacterium in group B.