Fermented tofu is a type of traditional Chinese food. The aim of this study was to compare the bacterial composition and its effect on the quality and safety of fermented tofu.Methods The total DNA was directly extracted from seven brand of fermented tofu samples produced in four provinces. The V3 region of 16S rRNA gene were amplified, and PCR products were mixed for pyrosequencing. Results According to the analysis of the sequences, Firmicutes, Proteobacteria, Bacteroidetes and Fusobacteria were predominant, accounting for 97.4% of all the bacteria. In terms of genus, most types of the fermented tofu had more than 10 genus members. It was also found that the composition of bacterial communities related to the geographic location and the production processes of fermented tofu. On the other hand, bacterial communities in some of fermented tofu showed relatively high abundance of pathogen or opportunistic pathogen, such as Klebsiella, Salmonella, Cronobacter, Vibrio, Enterobacter and Bacteroidetes.Conclusion These results suggested that the existing fermented tofu production model needed to be updated, and some products might have a risk of food safety.