Abstract: Lysine is able to inhibit growth of Microcystis aeruginosa(M.aeruginosa) significantly under illumination.To explore mechanism of the function,toxicological effect of lysine,different in concentration on M.aeruginosa was studied.Results show that the inhibiting effect varied with the strains,and followed the order of non-toxic strain>low toxic strain>high toxic strain.At the initial period,lysine did not have much influence on the anti-oxidative system(e.g.SOD and MDA) and integrity of the membrane of M.aeruginosa cells,but affected significantly the content of cytochrome(chlorophyll a and phycocyanobily) and activity of esterase.At the late period,the cells broke and died,with all the parameters changed significantly.Response of M.aeruginosa cells to lysine did not generate any common toxicological effects,like lipid peroxidation,but was a kind of orderly death process.