Recent animal and bird deaths at several lakes in Ireland were indicative of possible cyanobacterial poisoning. Using protein phosphatase inhibition assays, microcystins (MCs) were identified in extracts of cyanobacteria from several lakes at concentrations ranging from 1.6 to 168 µg/g. This is the first report of MCs in Irish freshwaters. The protein phosphatase inhibition assay was used to screen fractions during HPLC purification of the MCs in cyanobacteria (Anabaena and Oscillatoria) and water samples from Corbally and Caragh Lakes. MC-LR, MC-HtyR, MC-FR, and MC-YR and 3 unidentified MCs of m/z values 1028.5, 981, 1042.7 were isolated from the Corbally sample; while the Caragh Lake sample contained largely MC-LR and MC-YR. A new microanalytical technique was developed for the confirmation of MCs which involved the derivatisation of the methyldehydroalanine group of MCs with 2-aminoethanethiol. Electrospray mass spectrometry of these products showed characteristic double-charged ions, and this novel technique was useful for differentiating MCs from co-eluting impurities in HPLC fractions of cyanobacterial extracts.