In this work, mycosporine-like amino acids (MAAs) of Synechocystis sp. PCC 6803 were characterized and were investigated on UV induction and protective ability. High performance liquid chromatographic (HPLC) studies revealed three major compounds in the MAAs. By UV absorption and mass spectra analysis, one of the compounds was tentatively identified as mycosporine-tau (M-tau). One novel compound similar to usujirene was tentatively named as dehydroxylusujirene, and the other novel compound was named as M-343 according to its absorption maximum. In vivo experiments indicated that M-tau was induced by both UV-A and UV-B, while dehydroxylusujirene and M-343 were only induced by UV-A, suggesting that different chromophores were involved in MAAs synthesis in Synechocystis sp. PCC 6803. It was also indicated that M-343 could be photochemically synthesized from some precursors. Under both UV and oxidation stresses, M-343 was more stable than dehydroxylusujirene and M-tau. Considering the reaction with H2O2, M-tau and dehydroxylusujirene might be potential antioxidants in reaction with physiological reactive oxygen species in vivo. In protection experiments, the MAAs exhibited efficient protective ability towards UV-B and H2O2 stresses, with maximal protection rates of 30% and 21.5%, respectively. These results indicate that the MAAs in Synechocystis sp. PCC 6803 act as both UV-screen and antioxidant.