Abstract: Eutrophication leads a mass of algae, and algae bloom directly influence the ecological function of water bodies and the safety of drinking water. It is very important to control the growth and reproduction of blooming algae for fishery, industrial and agricultural production as well as for the health of humans. Although some methods have been proposed to control harmful algal growth, only a few are applicable due to high cost, secondary pollution, or impracticability. The commonly used algicides, such as copper (Cu2+) and organic herbicide, can inhibit the entire phytoplankton community and cause subsequent water quality deterioration that may stress or kill aquatic animals. Furthermore, copper might accumulate in the bodies of aquatic predators, and herbicides might be toxic to all the living species in the water body. Therefore, it is necessary to explore an effective and secure new method to control the growth of harmful algae. Submerged macrophytes can reduce harmful algae blooms to maintain clear water in natural and experimental aquatic ecosystems. Using allelochemicals, which were produced by some macrophytes, to inhibit the growth of some harmful algae has been reported, but the allelopathic effects of alkaloids from submerged macrophytes were not found. In this study, the alkaloids of Elodea nuttallii were extracted by ethanol and then fractionated with some chemical reagent. The alkaloids compounds were analyzed by gas chromatography- mass spectrometry (GC-MS). Mass fragments of the components were compared to the mass fragmentation data contained in the NIST 02. 9 alkaloids were identified from Elodea nuttallii by GC-MS, and the allelopathic effects of the alkaloids were also explored by bioassay of Microcystin aeruginosa. The alkaloids from Elodea nuttallii inhibited obviously to the growth of M. aeruginosa with the inhibition rate of 44.0% for three days, when the concentration of alkaloids were 62.0 mg/L. The alkaloids were a complicated mixture, which further purification was a challenging job. The detailed components of alkaloids were not clear now, but the result of bioassay showed that there were active constituents in alkaloids which provide a useful information for further study of the allelochemical in submerged macrophytes.