Abstract: Objective: To compare the PDT and light photosensitive effect between Phycobiliprotein Chromophore peptides and PhotofrinⅡ. Methods: Analyzed the spectroscope properties of R-phycoerythrin (R-PE) βsubunit, C-phycocyanin chromophore peptides CCP1、CCP3 and photofrinⅡ； The PDT effect of R-PEβsubunit on S180 cell, tumor bearing mice and light photosensitive effect on mouse marrow cell and daphnia were measured by MTT method. Result: There were multi-absorption peaks in photofrinⅡ between 250 nm ~ 650 nm, The higher absorption peaks were located in 250 nm ~ 450 nm; whereas, there are only one or two absorption peaks of Chromophore peptides R-PEβ,CCP1 and CCP3 in visible light area, the higher were located in 450 nm ~ 650 nm. In vivo test, in the condition of tumor diameter between 0.5 cm ~ 0.7cm and the irradiation dose of 120 J/cm2, the tumor inhibited rates of CCP1-CCP3 and photofrinⅡafter 7 days were 61 %、46 % and 81 %. In vitro test, when treated with 100 μg/ml photofrinⅡ, irradiated with 45 J/cm2, the survival rate of S180 cell and mouse marrow cell were 20 % and 33 %，whereas, when treated with R-PE βsubunit, the survival rate of S180 cell and mouse marrow cell were 65 % and 95 %; The phototoxicity of photofrinⅡ, CCP1 and CCP3 on the life of daphnia was time and dose dependent by using iodine-tungsten lamp as light source, photofrinⅡ showed stronger phototoxicity than CCP1 and CCP3. Conclusion: With the advantage in good light absorbent character, weak phototoxicity, better PDT effect and special fluorescence activity, R-PE βsubunit, CCP1 and CCP3 are the attractive option for improving the selectivity of PDT.