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Flavonoids are natural polyphenolic compounds from plants. As a new biotechnological algaecide, the molecular mechanism of plant flavonoids on the inhibition of Microcystis aeruginosa is still unknown. Therefore, in this study, we analyzed the variation of expressions of photosynthesis-related genes, microcystin synthesis-related genes and the genes involved in N and P acquisition in M. aeruginosa under the flavonoids stress. The results showed that the expression of psbD1, psaB and rbcL related to photosynthesis were influenced by three flavonoids but with different changing tendencies. The transcription of mcyA, mcyD and mcyH related to microcystin synthesis were decreased after 5-d of exposure, which could block microcystin synthesis. Meanwhile, flavonoids treatments resulted in the inhibition of N and P acquisition related genes transcription to affect the absorption of N and P in algal cells, and further …