Membrane separation technology is increasingly becoming an important innovation in biological wastewater treatment. Biofouling of the membrane is a major factor affecting the efficient and economic operation of membrane separation bioreactors (MBRs). This review summarizes the state-of-the-art progress in understanding the mechanisms and factors affecting membrane biofouling and the strategies for biofouling control. Biofouling mechanisms include the adsorption of soluble and suspended extracellular polymers on membrane surfaces and in membrane pores, the clogging of membrane pore structure by fine colloidal particles and cell debris, and the adhesion and deposition of sludge cake on membrane surfaces. Design and operating conditions of membrane modules and materials, hydrodynamic conditions in MBRs, process and environmental conditions of activated sludge systems, and the physicochemical properties of the wastewater are the dominant factors determining membrane biofouling. Current strategies to control biofouling include periodic relaxation, backwashing, chemical cleaning, and possible manipulation of hydrodynamic conditions and sludge properties. Achieving full integration of MBRs in wastewater treatment technology requires further research and development. Fundamental information on the bacteria, colloid, and membrane interaction, developed through multimethod and multiscale approaches, is particularly needed.