Abstract: The current study obtained four different allelopathic crude extracts from Pistia stratiotes Linn, a aquatic floating plant with higher efficiency on nitrogen and phosphorus removal, using ethanol ultrasonic extraction. These four, allelopathic extracts (0.1 g/L) inhibited the growth of Microcystis aeruginosa (FACHB-911) for 40%, 69%, 40% and 35% after 5 days treatment, respectively. Extracts were further purified through the method of acidic alumina column chromatography separation, which had inhibition rates 12%, 11%, 33 and 41% after 5 days treatment, respectively. Interestingly, one group of allelopathic fraction had 80% inhibition rate after 5 days treatment. The results of gas chromatography-mass spectrometry (GC-MS) analysis revealed that the extracts from P. stratiotes mainly contained two antialgal compounds including P-toluene sulfonic acid methyl ester and stearic acid amide.