The bacterial community structure of three types Fen-Daqus (Qingcha Daqu, Houhuo Daqu and Hongxin Daqu) were studied through construction of bacteria 16S rRNA gene clone library, sequencing and phylogenetic analyses. The results showed that the bacteria communities of three types Fen-Daqus were both distributed in Bacilli, Actinobacteridae, Gammaproteobacteria. But there are some specific differences in detail composition of the bacterial species among the three types Fen-Daqus. Lactobacillus and Staphylococcus were the dominant bacteria in Qingcha Daqu (the ratio to total clones were 37.78% and 22.22% separately); Lactobacillus, Staphylococcus, Bacillus and Weissella were the dominant bacteria in Houhuo Daqu (the ratio to total clones were 35%, 16.67%, 16.67%, 13.33% separately); Lactobacillus, Bacillus and Thermoactinomyces were the dominant bacteria in Hongxin Daqu (the ratio to total clones were 26.67%, 28.89%, 17.78% separately).