The growth of Potamogeton pectinatus and P. malaianus in waters with a great number of cycanobacteria was studied through some micro-ecosystems and a large enclosure (6667 m²). The results of the micro-ecosystems experiment showed that influence of cycanobacteria on P. pectinatus was not Significant. Biomass of P. pectinatus only decreased 8.4% when it grew in waters with a great number of cycanobacteria in 22 days, but biomass of P. pectinatus increased 27.7% in waters without cycanobacteria. And that of cycanobacteria on P. malaianus was Significant. Biomass of P. malaianus decreased 57.1% when it grew in waters with a great number of cycanobacteria in 22 days, whereas Biomass of P. malaianus in waters without increased 24.1%. The results of the large enclosure experiment showed that the cover rate of was up to 60% under the condition of pressure with a great number of cycanobacteria. However, P. malaianus diedont under the same condition. Therefore, the results of above indicated that impact of cycanobacteria on P. pectinatus was less pronounced than that on P. malaianus.