The purpose of this study was to extract phycobiliproteins (PBP) from Porphyra yezoensis using an optimized procedure and further establish a large scale process for protein production. According to our previous experiences on the extraction of PBP, salting out methods, e.g. ammonium sulfate precipitation, worked more efficiently than isoelectric precipitation, differential centrifugation or ultrafiltration. Thus, we chose ammonium sulfate to coprecipitate PBP in crude solution. After four times of precipitation followed by one time of high speed centrifugation, the maximum purity of crude phycoerythrin and phycocyanin reached 1.94 (A 565 /A 280 ) and 0.85 (A 615 /A 280 ), with a yield of 0.50% and 0.37%, respectively. A total of 0.94 mg phycoerythrin and 0.54 mg phycocyanin with purity of more than 3.2 were obtained from 1 g dried P. yezoensis after additional chromatography. We further scaled up the frozen dried P. yezoensis from 20 g to 400 g, with 1295 mg phycoerythrin and 593 mg phycocyanin obtained.