In this study, a mixture of ozone and air (ozonation air for short) was adopted for the inactivation of Microcystis aeruginosa in a sequencing batch reactor (SBR). Scanning electron microscopy of Microcystis aeruginosa revealed damage to the cell wall and leakage of intracellular contents after ozone oxidation. Owing to the destruction of cells, the chlorophyll a released from the cells was degraded by ozone oxidation, which showed that chlorophyll a concentrations increased vastly during the first 5 min, then, decreased continuously. pH in the SBR declined with increasing time, reaching around 3.0 at the end of the cycle. It was observed that the removal efficiencies of chlorophyll a were, respectively, 68.4%, 74.5%, 86.7% and 77.9% after 90 min at pH 3.0, 7.0, 9.0 and 11.0 conditions, and the degradation of chlorophyll a accorded with the apparent first-order kinetics. The results suggested that inactivation of Microcystis aeruginosa was successfully performed by ozone treatment, verifying the potential of this alternative process for the decontamination of eutrophic water. (C) 2010 Society of Chemical Industry