The applicability of capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) methods for the simultaneous determination of two frequently occurring microcystins (MCs-LR and -YR) and a new variant (MC-YA) in crude extracts of Hungarian bloom samples and cyanobacterial cultures was studied. It was found that the comparison of the results obtained by both CZE and MEKC measurements (due to the differences in their separation mechanisms) for the same sample can guarantee the reliability of the quantitative results. In our work environmental samples like lake waters, water bloom samples, cyanobacterial isolates were analysed. The three microcystins could be directly determined in water bloom samples collected from Hungarian lakes and laboratory culture samples of cyanobacteria.