R-phycoerythrin was purified by means of phenyl-sepharose expanded bed absorption and DEAE-sepharose ion-exchange chromatography from Porphyra yezoensis, one of the largest and important aquaculture species in China. Final R-phycoerythrin preparation was characterized by purity ratio above 4 and the homogeneity in native PAGE, respectively. The results of absorption spectrum, fluorescence spectrum and SDS-PAGE were in agreement with previous reports on R-PE. The yield of R-phycoerythrin was 0.82 mg g−1 wet leafy gametophyte of P. yezoensis. This method is a high-protein recovery technology while reducing processing time, and is suitable for the large batch production of R-phycoerythrin, which will enhance the value of P. yezoensis in China, especially the inferior P. yezoensis which can not be used for flake processing.