The growth of Microcystis aeruginosa UTEX 2388 was repressed by ultrasonic radiation and resulted in an increased chlorophyll a content and cell size, suggesting the inhibition of cell division. However, growth was recovered immediately after the interruption of ultrasonication. In addition to the disruption of gas vesicles, other mechanisms of growth inhibition were also investigated. Although free radicals were produced by ultrasonication and hydrogen peroxide, the resulting lipid peroxidation in the cells was not comparable, indicating minimal damage by the free radicals. Ultrasonic radiation late in the day was found to be most effective in reducing the growth rate of M. aeruginosa, and this timing also corresponded to the phase of daily cell division. In an enclosure experiment, ultrasonic radiation reduced the pH, DO, total nitrogen, and total phosphorus, whereas it increased the water temperature, conductivity, and orthophosphate concentration. The algal cell density and chlorophyll a concentration drastically decreased after 3 d of ultrasonication, plus the cyanobacterial proportion was selectively reduced as compared to other algal species. Accordingly, ultrasonic radiation would appear to have considerable potential as an effective control method for cyanobacterial blooms.