This paper studied the ultrasonic removal of indigenous blue-green algae taken from Lake Taihu. The results showed that higher ultrasound frequency benefited the removal of indigenous algae. But in consideration of complex condition of the natural lakes and reservoirs such as the lack of powerful electrical supply system, low sound frequency is more suitable. Because of slightly improvement in the algae removal rate constants among the low frequency range (20-100 kHz), 20 kHz is the best ultrasound frequency for indigenous algae removal. Moreover, little change in the microcystins concentration was found with sonication at 20 kHz, 2W for 60s, which was compared with the increased microcystins from 2.67 to 2.851 mg/L after sonication at 1000 kHz, 2W for 60s. the concentration of chlorophyll.