We explored the possibility of using allelochemicals from terrestrial plants to solve the problem of cyanobacterial blooms in eutrophicated shallow lakes. The highly effective inhibitory allelochemicals of purslane (Portulaca oleracea L.) and purslane seeds were extracted and purified through a series of procedures, and the chemical components of the purified extracts were analyzed by gas chromatographymass spectrometry (GC-MS). The extracts contained 12 fatty acids and three phenolic acids, of which nine compounds were found to be inhibitors of harmful cyanobacteria. The inhibitory ratios of the purified extracts of purslane and purslane seeds on M. aeruginosa were 97.4 and 81.6%, respectively, when the cyanobacterial were exposed under 15.0 mg/L of extracts. The purified extracts exhibited significant anticyanobacterial activities, the organic acids that may contribute to the allelopathic effects of the purslane and purslane seeds on M. aeruginosa.