Capillary zone electrophoretic and micellar electrokinetic chromatographic methods with UV detection were investigated for separation and identification of some microcystins isolated from cyanobacterial Anabaena 90 strains in Finland. The low-sensitivity purity tests with full scan UV–Vis spectra were done with a CZE method. All the test compounds, [d-Asp3,Dha7]MCYST-LR, MCYST-LR, MCYST-YR, [Dha7]MCYST-LR, MCYST-RR, [Dha7]MCYST-RR, [d-Asp3,Dha7]MCYST-RR, [d-Asp3]MCYST-LR and [d-Asp3]MCYST-RR (where MCYST stands for microcystin) isolated with a preparative HPLC method, could be separated from each other in a MECC method. The detection limits of the microcystins were below ppm level. The repeatability of the MECC technique was tested by comparing the absolute migration times with the indices calculated with “in-laboratory” designed programs operating in MATLAB Mathworks Inc. The identification and the high-sensitivity purity tests of the isolated microcystins were made with an off-line electrospray mass spectrometer. Identification could be done for MCYST-YR, MCYST-LR, MCYST-RR, [Dha7]MCYST-RR, [Dha7]MCYST-RR, [d-Asp3]MCYST-LR, [d-Asp3]MCYST-RR, [d-Asp3, Dha7]MCYST-LR and [d-Asp3, Dha7]MCYST-RR on the basis of their [M+H]+ or [M+2H]2+ ions in the MS mode and by using the protonated molecule as precursor in the MS–MS mode.