Abstract: Eutrophication directly leads to the explosion of algae. The ecological function of water bodies might be damaged by algal blooms. The safety of drinking water could also be threatened by algal blooms. The ecological floating-bed is widely used to control harmful algal blooms. Canna indica is one of the most widely used plants in the technology of ecological floating-beds to treat eutrophication. The root secretions of C. indica were investigated for their inhibitory effects on the growth of Microcystis aeruginosa by adding the former to the culturing of the latter. The results showed that:1) The growth of M. aeruginosa was significantly inhibited by the root secretions of C. indica. The highest inhibitory rate (64.4%) could be reached within 20 days. The ρ(Chla) of the controls could be 1.98 times that of the experiment. 2)The results of GC-MS (gas chromatography-mass spectrometry) analyses showed that there were 10 fatty acids in the root secretions of C. indica. The contents included hexanoic acid, palmitic acid and octadecanoic acid. There were 19 compounds in the root extraction of C. indica. 3)The acids included DL-Lactic acid, 3-methoxy-4-hydroxycinamic acid, linoleic acid and palmitic acid. The fatty acids played important roles in inhibiting the growth of M. aeruginosa.