Membrane bioreactor (MBR) provides the benefits on high effluent quality and construction cost without the secondary clarification. Despite of these advantages, fouling, which clogs the pore in membrane modules, affects the membrane life span and effluent quality. Studies on the laboratory scale MBR were focused on the control of particulate fouling, organic fouling and inorganic fouling. However, less studies were focused on the control of biofouling and microbial aspect of membrane. In the full scale operation, most MBR produces high effluent quality to meet the national permit of discharge regulation. In this study, the performance and microbial community analysis were investigated in two MBRs. As the results, the performance of organic removal, nitrogen removal, and phosphorus removal was similar both MBRs. Microbial community analysis, however, showed that Azonexus sp. and Propionivibrio sp. contributed to indirect fouling to cause the chemical cleaning in the DX MBR.