Recently, there have been many intensive studies on the release route of allelochemicals from terrestrial plants. Leaf leaching and volatilization of the aerial parts were found to be the main release routes (Miller and Gorchov 2004; Hao et al. 2007). However, our results showed that the root exudates from the aquatic plant of P. stratiotes exhibited the best algae growth-inhibitory effect. The second most effective routes were residue decomposition and leaf leachates, while leaf volatilization showed no algae growth-inhibitory effect. The similar result also had been found in the aquatic plant of water hyacinth; the root of water hyacinth could release many anti-cyanobacteria allelochemicals (Malik 2007; Mulderij et al. 2007). The difference might be caused by the different growth environment and physiological structures of terrestrial and aquatic plants. Therefore, research into the ideal release route for different types of plants to effectively control algae growth has essential instructional significance. In the present study, we simulated the release route of allelochemicals from aquatic plants in the natural environment. Water was used as a solvent for the leaching, secretion, and extraction of allelochemicals. The simulation was close to the true growth environment of the aquatic plant. However, the results only showed that more water-soluble allelochemicals existed in the roots than in the leaves. Other allelochemicals that have lower water solubility in other parts require further study. Furthermore, the water and microbes in natural environment have certain effects on root exudates and residue decomposition. Thus, further investigation is needed to elucidate whether the anti-cyanobacteria allelochemicals are directly released from plants or indirectly generated by the effects of water and microbe.