Abstract: Gel filtration to the extracted phycobiliprotein solution from Polysiphonia urceolata rich in phycoerythrin was performed by four gels of Sephadex G-150 ( G-150) , Sephadex G-200 ( G-200) , Sephacryl S-200 ( S-200) and Sephacryl S-300 ( S-300) , and the obtained fraction of phycocyanin and allophycocyanin was further purified by the gel filtration on G-150, S-300 and S-200.An optimized technical procedure of isolating phycocyanin and allophycocyanin from the extracted phycobiliproteins of Polysiphonia urceolata by the gel filtration in turn on G-150, S- 300 and S- 200 was established based on the experiments.By the procedure, the phycoerythrin was efficiently separated and the phycocyanin and allophycocyanin were purified to such a degree that the relative content of phycocyanin and allophycocyanin in the obtained fraction increased with respect to the extracted phycobiliproteins solution.The relationships of practical gel filtration effects with some main factors of gel column, such as selectivity, efficiency and the inside volume, and the constituents of protein samples were discussed on the basis of observed phenomena in the experiments.