Extracellular polymeric substance (EPS), as a major component of microbial assemblages, e.g., activated sludge, biofilm and particulate sludge, etc., plays a crucial role in the formation and structural maintenance of microbial assemblages. Extracellular protein is a main constituent of EPS, and its functioning in microbial flocculation and aggregation has being paid more and more attention. The development and application of protein analytical techniques provide a good platform for the further study of extracellular protein. The paper reviewed the kind and distribution of extracellular protein in microbial assemblages and the roles of the extracellular protein in flocculation, sedimentation, adsorption, mass transferring, and dewatering. The prospects of the future study and applications of extracellular protein were also put forward.