The application of hydrogen peroxide (H2O2) as a management tool to control Microcystis blooms has become increasingly popular due to its short lifetime and targeted action. H2O2 increases intracellular reactive oxygen species resulting in oxidative stress and subsequently cell death. H2O2 is naturally produced in freshwater bodies as a result of photocatalytic reactions between dissolved organic carbon and sunlight. Previously, some studies have suggested that this environmental source of H2O2 selectively targets for toxigenic cyanobacteria strains in the genus Microcystis. Also, past studies only focused on the morphological and biochemical changes of H2O2-induced cell death in Microcystis with little information available on the effects of different H2O2 concentrations on growth, esterase activity and membrane integrity. Therefore, this study investigated the effects of non-lethal (40-4000 nM) concentrations on percentage cell death; with a focus on sub-lethal (50 μM) and lethal (275 μM; 500 μM) doses of H2O2 on growth, cells showing esterase activity and membrane integrity. The non-lethal dose experiment was part of a preliminary study. Results showed a dose- and time-dependent relationship in all three Microcystis strains post H2O2 treatment. H2O2 resulted in a significant increase in intracellular reactive oxygen species, decreased chlorophyll a content, decreased growth rate and esterase activity. Interestingly, at sub-lethal (50 μM H2O2 treatment), percentage of dead cells in microcystin-producing strains was significantly higher (p