Cyanobacteria are photosynthetic bacteria with some characteristics of algae. Some cyanobacteria produce toxins that have been shown to be hazardous to both animals and humans. Previous research has demonstrated power ultrasound can provide a suitable method to control algae blooms although the optimum ultrasonic parameter settings have not been determined to ensure an effective and energy efficient treatment. In this work the effect of ultrasound on suspensions of Microcystis aeruginosa has been investigated at the following frequencies 20, 40, 580, 864 and 1146 kHz. Results showed that the reduction in algal numbers is dependent on both frequency and intensity. In order to quantify the effect we have defined the efficiency of the ultrasonic control of algae at a specific frequency as: (% inactivation of the algae) / (ultrasonic intensity applied). When this is applied to the results at different frequencies the order of efficiency for algae reduction is 20 < 1146 < 864 < 580 kHz. This suggests that ultrasound can offer a suitable method for algae inactivation or control but the sonication conditions must be taken into account.