Eichhornia crassipes (Mart.) Solms has been applied widely to assimilate nutrients and coexisted with blooming cyanobacteria (mainly Microcystis aeruginosa) in many eutrophic lakes. But the effect of E. crassipes on hepatotoxic microcystins production in cyanobacteria still needed to be made clear. In this study, the effect of E. crassipes on DNA damage and transcription of microcystin biosynthetic genes in M. aeruginosa were first investigated and the links between microcystins production and other biochemical characteristics in M. aeruginosa were also explored. Results showed that the relative transcript levels of mcyA and mcyB in M. aeruginosa under stress of E. crassipes were stimulated briefly and then soon inhibited, while that of mcyD was motivated fleetingly and then kept at same level as controls. The accumulation of DNA damage in M. aeruginosa was exacerbated at state of energy limitation resulted from stress of E. crassipes and then triggered death via apoptosis. The transcription of microcystin biosynthetic genes in M. aeruginosa was not completely regulated by oxidative stress. It needed active photosynthetic electron transfer which could be blocked by E. crassipes. Furthermore, poor repair of oxidative DNA damage in M. aeruginosa inhibited the expression of microcystin biosynthetic genes under exposure of E. crassipes.