<jats:title>Abstract</jats:title><jats:p>Cyanobacteria, also called blue‐green algae, occur worldwide within water blooms in eutrophic lakes and drinking water reservoirs, producing several biotoxins (cyanotoxins). Among these, microcystins (MCs) are a group of cyclic heptapeptides showing potent hepatotoxicity and activity as tumour promoters. So far, at least 89 MCs from different cyanobacteria genera have been characterised. Herein, ion trap, matrix‐assisted laser desorption/ionisation time‐of‐flight (MALDI‐ToF) and quadruple time‐of‐flight (Q‐ToF) mass spectrometry (MS)‐based methods were tested and compared for analysing MCs in freshwaters. Method performances in terms of limit of detection, limit of quantification, mean recoveries, repeatability, and specificity were evaluated. In particular, a liquid chromatography/electrospray ionisation (LC/ESI)‐Q‐ToF‐MS/MS method was firstly described to analyse MCs in freshwaters; this technique is highly selective and sensitive, and allowed us to characterise the molecular structure of an unknown compound. Indeed, the full structural characterisation of a novel microcystin variant from a bloom of <jats:italic>Planktothrix</jats:italic> <jats:italic>rubescens</jats:italic> in the Lake Averno, near Naples, was attained by the study of the fragmentation pattern. The new cyanotoxin was identified as the 9‐acetyl‐Adda variant of microcystin‐RR. Copyright © 2009 John Wiley & Sons, Ltd.