A Microcystis aeruginosa which produced high content of microcystin-LR (MC-LR) but no microcystin-RR (MC-RR) was isolated from Dianchi Lake in China. In the molecular structure of MC-LR, glutamic acid, aspartic acid, leucine, alanine and arginine are the constitutional components which are abundant in natural water. In this paper, effects of six amino acids at their natural concentrations on the growth of the M. aeruginosa and the microcystin (MC) production were studied in batch culture. M. aeruginosa could assimilate alanine, leucine and arginine as sole nitrogen sources for growth and MC production. However, glutamic acid, aspartic acid and lysine could not be assimilated quickly, although they could pass the cell membrane and enter into the cell rapidly. Our experiment demonstrated that the possible reason of such phenomenon was that different amino acids had different effects on the process of metabolism through the free dissolved amino acids within the cells. (C) 2008 Elsevier B.V. All rights reserved.