Chloride and carbonate salts are the main salts causing salinization and widely exist in aquatic environment, so algae may suffer from salinization stress for high water evaporation. In this study, in order to investigate and compare the toxic effects of the two salts on algal photosynthesis, we used NaCl and Na2CO3 to stress Chlamydomonas reinhardtii. Under the two salt stresses, the content of O
−.2 and H2O2 in the cells was increased significantly, and it was much higher in Na2CO3 treatment than in NaCl treatment at the same Na + concentration. The absorbance spectra and 4 th derivative spectra of photosynthetic pigments were declined under 300 mM NaCl and 25 mM Na2CO3 stresses, and remarkably changed under 50 mM and 100 mM Na2CO3 stresses. When the cells stressed by the two salts, the maximum quantum yield (Fv/Fm), electron transport rate (ETR) and photochemical quenching (qP) were reduced markedly, but the nonphotochemical dissipation (NPQ) was increased markedly. At the same Na + concentration, Na2CO3 stress had stronger toxic effects on photosynthetic ability than NaCl stress.