From analytical to commercial scale, aqueous two-phase systems have their application in the purification, characterization and study of biomaterials. In order to improve the selectivity of the systems, the biospecific affinity ligands were introduced. In the affinity partitioning aqueous two-phase system, have many enzymes been purified. This review discusses the partitioning of some enzymes in the affinity aqueous two-phase systems in regard to the different ligands, including reactive dyes, metal ions and other ligands. Some integration of aqueous two-phasesystem with other techniques for more effective purification of enzymes are also presented.