The increasing incidence of cyanobacterial blooms with their associated production of cyanotoxins lead managers of aquatics systems to control their biomass to limit the health risk. Among the variety of existing treatment approaches, hydrogen peroxide (H 2 O 2 ) shows increasing use but the effects of environmental parameters on its effectiveness are still not completely known. With the aim to assess the efficiency of H 2 O 2 treatments in the control of cyanobacterial blooms and decrease toxic risk, we tested three Microcystis strains according to their ability to produce cyanotoxins (a microcystin-producing, non-microcystin-producing and mcyB-knockout mutant). Photochemical efficiency, percentage of living cells and microcystin cell content were compared under various hydrogen peroxide concentrations coupled with stress conditions encountered during the life cycle of cyanobacteria as darkness and high light. The microcystin-producing strain appeared the more sensitive to hydrogen peroxide treatment and to light condition, probably due to a lower rate of repair of Photo System II (PSII). We also highlighted various responses of PSII activity according to Microcystis strains which could partly explain the shift of dominant genotypes often occurring during a bloom event. Our results confirm the link between light and microcystin content and variations of microcystin contents appear as a consequence of photosynthetic activity. These findings could be of particular interest regarding water quality management, especially the use of H 2 O 2 as a potential algaecide which seems to be more effective to use during periods of high light.