The phycoerythrin (R-PE) is a fluorescent protein, which has great commercial and industrial value. In order to obtain a high purity R-PE which above the food grade standard, the R-PE was separated and purified from the Porphyra haitanensis using aqueous two-phase system (ATPS). At the optimal conditions of polyethylene glycol (PEG) of 1500 in the ATPS (potassium sodium tartrate/PEG), pH of 8.06, the tie-line length (LTL) of 22.30% and volume ratio (V_r) of 0.12, purity of the isolated R-PE would increase from 0.43 (initial purity) to 1.47 after the first extraction, with a recovery rate of 84.42%. After the second ATPS extraction, achieved a purity and purification factor of 1.55 and 3.60, respectively. The isolated R-PE had a high biological activity. It was a successful purification process for R-PE for industrial application, with the advantages of high efficient and low cost.