Abstract: Allelopathic inhibitory effects of different amounts of root and planting water of Anthurium on Microcystis aeruginosa were comparatively studied. The results showed that large amounts (3.0 and 4.0 g/L) of Anthurium root could effectively inhibit the growth of M. aeruginosa, with inhibition rates over than 90%. The photosynthetic activity of M. aeruginosa was greatly affected. The Φmax, Φ and ETR were reduced compared to the control group. The enzyme system of M. aeruginosa cells was also inhibited after the treatments. The cell membranes and organelles membranes were attacked by free radicals seriously. MDA accumulated rapidly and POD was reduced drastically. The inhibition rates increased along with the increase of root amounts. Compared with the control group, the light quantum yield of the experimental groups with high amounts of Anthurium root was reduced by 0.3, yet c(MDA) increased over 10 nmol/mL and activities of POD decreased nearly 3 U/mg. At the end of the 18^th day of the experiment, the ρ(Chla) of the control group and the 0.5,1.0,2.0,3.0,4.0 g/L root treated groups were 515.80,6.35,6.44,0.50,3.67 and 4.13 μg/L respectively. The planting water of Anthurium could inhibit the growth of M. aeruginosa, but the inhibitory effect was worse than that of root with high amounts.