Purification of water containing pesticide namely Malathion in membrane bioreator has been carried out. To understand the complex fouling mechanisms and fouling propensities occurring in a Membrane Bioreactor (MBR), in the current work, comparison of malathion degradation by single species, Pseudomonas Stutzeri, and microbial consortium has been carried out. Extracellular Polymeric Substances (EPSs) and Soluble Microbial Proteins (SMPs) are considered to increase the fouling. Experimental results revealed 85-90% reduction in the COD of the malathion containing synthetic wastewater and degradation kinetics has been reported. Complete reduction of malathion observed within 24 h in both the cases. A key parameter, critical flux is found to be 10 LMH for both the membrane bioreactor systems. Cake and Membrane resistances are calculated thus giving an insight regarding the working of Membrane Bioreactor based on single species and activated sludge.