The effects of a newly isolated quorum quenching (QQ) bacteria (Bacillus sp. T5) on the microbial community has been evaluated via the Illumina sequencing method. Membrane bioreactors (MBRs) operated with this novel QQ bacterium to evaluate the improvement in the performance of MBR. Anti-biofouling effect of T5 was enhanced as 71% compared to the control reactor. Also, QQ bacteria did not have any negative effect on the removal of organics during the process. Gram-negative bacteria were found to be dominant over Gram-positive bacteria. Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, and Chloroflexi were dominant phyla in the control and QQ reactors. The proportion of Alphaproteobacteria was most significant among Proteobacteria. The relative abundances of Actinobacteria, Acidobacteria, and Firmicutes were significantly affected by Quorum quenching mechanism. On the other hand, QQ activity of Bacillus sp. T5 significantly influenced the relative abundance of Proteobacteria, Bacteroidetes, and Chloroflexi. The QQ process appeared to generate variations in the structure of the microbial community. According to the results of the molecular analyses, the syntrophic interaction of Bacillus sp. T5 and indigenous Gram-negative and Gram-positive bacterial community is critical to the performance of MBRs.