The sensitivities of Selenastrum capricornutum and the toxic strain Microcystis aeruginosa to exudates from Potamogeton maackianus and P. malaianus were compared using exudation experiment, and the potential allelochemicals released by these two pondweeds into surrounding water were also analyzed. The growth of S. capricornutum and M. aeruginosa was inhibited by the exudates from the two macrophytes. Compared to the control, the cell densities of S. capricornutum decreased by 42.7% and 61.9% in 2.5 and 5 g·L^-1 FW P. maackianus treatments, and the cell densities of S. capricornutum also decreased by 65.8% and 73.5% in the two biomass density treatments of P. malaianus after three days of treatments. After 3 days’ incubation in 2.5 and 5 g FW·L^-1 P. maackianus exudates, the M. aeruginosa cell densities were higher in control than in treatment. As for P. malaianus treatments, the cell densities of M. aeruginosa were reduced by 16.5 and 65.8% of the control in 2.5 and 5 g·L^-1 FW marophytes at the end of incubation period, respectively. The allelochemicals exuded from the macophytes, which inhibited both S. capricornutum and M. aeruginosa, belonged to lipophilic and moderately lipophilic compounds according to the bioassay results of exudate fractionations. By multiple comparison statistics, the results showed that P. maackianus had stronger inhibitory effects on M. aeruginsa, while S. capricornutum was more sensitive to the allelochemicals of P. malaianus. The different sensitivities of the two algae were probably caused by three alcohol compounds (1-methoxy-2-methyl-2- Propanol, 2-methyl-2-Hexanol, and 4-ethyl-2,6-dimethyl-4-Heptanol) through the GC-MS analysis of the most active exudate fractions.