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The phytogenic algicide sanguinarine shows strong inhibitory effects on some bloom-forming cyanobacteria and exhibits great potential in cyanobacterial bloom mitigation. To evaluate the possible ecological effects of sanguinarine on microalgae, the effects and possible mechanisms of sanguinarine on the competition between bloom-forming cyanobacterium Raphidiopsis raciborskii (formerly named Cylindrospermopsis raciborskii) and green alga Scenedesmus obliquus were investigated through co-culture competition test and comparative toxicological study including growth characteristics, chlorophyll fluorescence transients, activities of antioxidant enzymes, and lipid peroxidation. The results of Raphidiopsis-Scenedesmus co-culture competition test showed that sanguinarine decreased the competition ability of R. raciborskii , which benefitted S. obliquus in winning the competition. Toxicological studies have shown that sanguinarine exhibited high inhibitory effects on the growth and photosynthesis of R. raciborskii but no obvious toxicity on S. obliquus at concentrations of no more than 80 μg L−1. Oxidative damage partially contributed but was not the primary mechanism for the toxicity of sanguinarine on R. raciborskii. The results presented in this study indicate that sanguinarine may be a good algicidal candidate in mitigation of Raphidiopsis -based water bloom. Image 1 • The toxicity of sanguinarine on Raphidiopsis is far stronger than that on Scenedesmus. • Sanguinarine damages the electron-donating side of the PSII reaction center of Raphidiopsis. • Oxidative damage is partially responsible for the toxicity of sanguinarine on Raphidiopsis. • Sanguinarine decreases the competition ability of Raphidiopsis. [ABSTRACT FROM AUTHOR]