Cyanobacteria (blue-green algae) have been shown to produce unique biologically active peptides such as microcystins, mainly from different species of Microcystis aeruginosa. Presence of these toxic peptides (hepatotoxin) in fresh water supplies are of increasing concern and has emphasized the need for a suitable analytical method. Amounts of microcystin-LR were estimated in the laboratory cultures of PCC strains viz. PCC-7806, 7820, and PCC-7941, using high performance liquid chromatography. The identity of microcystin-LR was confirmed by LC-ESI-MS. The lower detection limit of quantification is 1.0 mg=L.