Membrane bioreactors (MBRs) are rapidly becoming the technology of choice over conventional activated sludge treatment systems due to their smaller footprint, reduced sludge production, rapid start-up of biological processes, complete removal of suspended solids and better effluent quality. The retention of sufficient amount of slow-growing nitrifiers makes it feasible for the MBRs to achieve strong tolerance against the shock loads with stable and highly efficient nitrogen removal. Various studies have focused on the ecophysiology of nitrifiers in MBRs as well as their distinctive operational parameters as well as their impact on the selection and activity of nitrifying community. Several techniques have been employed over the years to understand the nitrifying community and their interaction within the MBR system, which led to its modification from the initial design. This review focuses on the identification of optimal operational and environmental conditions for efficient nitrification in MBRs. The advantages and limitations of different techniques employed for investigating the nitrifying communities in MBRs are also emphasized.