Low concentrations of L-lysine and L-lysine-containing-peptides strongly inhibited the growth of axenic strains of 4 species belonging to the genus Microcystis (cyanobacteria). Inhibitory activities decreased in the order of L-lysine>tri-L-lysine>di-L-lysine>α-poly-L-lysine>L-lysyl-L-histidine>L-lysyl-L-alanine. The addition of 50 μM of L-lysine to growing cells of axenic strains of M. novacekii TAC20-1 and M. viridis NIES102 resulted in a loss of buoyancy, a decrease in chlorophyll a content and consequent cell lysis. The cells took up most of the L-lysine added to the culture medium of M. viridis NIES-102 in one day. However, the amino acid was released back into the medium with cell lysis 3 days after the addition. Laboratory results were confirmed in experimental ponds outdoors by spraying L-lysine onto natural Microcystis blooms in the summer of 1999 and 2000. The spraying of 50 μM L-lysine caused Microcystis colonies to vanish from the surface water within two days; there was a dramatic change in the color and transparency of the pond surface water. After the immediate disappearance of Microcystis sp., both Euglena sp. and/or Phormidium tenue appeared, the latter becoming the dominant species in the phytoplankton community of the pond. In the experiment in summer 2000, the L-lysine provided to the pond was assayed. The level decreased gradually and L-lysine was not detected in the pond water after 6 days. The mechanisms of growth inhibition by L-lysine and a possible mitigation of Microcystis blooms by the amino acid are discussed.