A suitable Aqueous Two Phase System (ATPS) has been identified for the partitioning of crude fish proteins from fish processing industrial effluent. A detailed study has been performed to analyze the influence of various parameters on protein partitioning such as molecular weight of PEG, effect of different salts (MgSO4 , K 2 HPO 4, Na 3 C 6 H 5 O 7, Na 2 SO 4, (NH 4 ) 2 PO 4, K 3 C 6 H 5 O 7 ) and their concentrations, pH, temperature, Tie Line Length (TLL), effluent loading and volume ratio. PEG 2000 -sodium sulphate ATPS was found to be a most favourable system among the selected ATPS for higher partition coefficient of proteins. The binodal curve and equilibrium characteristics of PEG 2000 -sodium sulphate were established and fitted to empirical equations. The equilibrium compositions (tie line) were correlated using Othmer-Tobias and Bancroft equations.