The application of capillary electrophoresis and of reversed-phase liquid chromatography coupled to electrospray mass spectrometry is presented for the analysis of microcystins isolated from toxic strains of Microcystis aeruginosa. The separation performance of these two techniques is compared in terms of both sensitivity and of resolution of closely related microcystins. Quantitation of microcystin-LR present at low micrograms/ml concentrations in cell extracts is demonstrated using both techniques. A marked advantage of capillary electrophoresis over liquid chromatography was its ability to resolve different desmethyl microcystin-LR analogues. Identification of these positional isomers was facilitated using capillary electrophoresis combined with tandem mass spectrometry (MS-MS). Rationalization of fragment ions observed in MS-MS spectra of microcystins was made possible through comparison with 15N labelled microcystins obtained from stable isotope feeding experiments. The potential of tandem mass spectrometry in providing selective detection of microcystins in cell extracts, and in structural characterization of novel microcystins, was also investigated.