Many measures have been developed to control the harmful algal blooms that are potentially threatening potable waters. The pilot experiments showed that the unfiltered and the sterile-filtered decoctions of Radix Astragali inhibited the growth of Microcystis aeruginosa. The inhibitory effect diminished in natural pond conditions after 68 days, due to photo-degradation of the flavonoids from Radix Astragali that appear to be responsible for the action on M. aeruginosa. Four phases (assemblage, conglomeration, cell membrane destruction and decomposition) can be characterized in the process of cell death with increasing decoction dose. The quantum yields and electron transport rates of photosynthesis system II of M. aeruginosa cells markedly decreased during contact with the decoction, resulting in the disruption of M. aeruginosa photosynthesis. The results indicate that the application of Radix Astragali decoction for the inhibition of M. aeruginosa growth is feasible when the dose is less than 20Â mlÂ L-1.