Abstract: In order to understand the influence of the blooming of Microcystis aeruginosa on the contents and sources of organic matter (OM), amino acids in the overlying water samples were collected from the eutrophic Meiliang Bay in the northern part of Lake Taihu. The growth process of M. aeruginosa in the water samples was simulated in the laboratory. The influences of the release of amino acids from M. aeruginosa on nutrients, amino acid and OM of the water were analyzed. The contents of fifteen amino acids including D-and L-of amino acid were determined by the pre-column derivatization with o-phthaldialdehyde (OPA) combined with HPLC. The contributions of amino acids and OM produced by M. aeruginosa to the organic matter, total carbon (TC), and dissolved total nitrogen (DTN) were investigated. The results showed that the contributions of M. aeruginosa-derived amino acid to TC, DTN and TOC in the overlying water were 23%-37%, 46%-93% and 46%-83% respectively. The concentration of the refractory amino acids (i.e., glycine, serine, alanine and lysine) was 60.4 μmol/L, which was much higher than the concentration (40.9 μmol/L) of degradable amino acids (i.e., tyrosine, phenylalanine, glutamic acid and arginine). The ratio of D-AA to L-AA decreased from 0.28 to 0.09, which indicated that the degradation degree of organic matter decreased during the period from logarithmic growth phase to decline phase. The results showed that the contents of amino acids increased as the degradation degree of the organic matter decreased. Therefore, large amounts of undegraded amino acids are an important source of organic matter in the overlying water. These results are fundamental to understanding the contributions of algae blooming to endogenous OM and nutrients, which is useful for understanding the cycling of nutrients in lakes.