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Microcystins are cyclic peptide hepatotoxins that are produced by several genera of cyanobacteria. We briefly review the molecular structural features of 67 reported cyclic heptapeptide microcystins and a related cyclic pentapeptide toxin. These substances present a significant analytical challenge because multiple toxins are often found in any given cyanobacteria or water sample, and it is likely that some structural variants have yet to be identified. We briefly describe a hybrid linear ion trap – Fourier transform ion cyclotron resonance (LT-FT-ICR) mass spectrometer equipped with a liquid chromatography (LC)/electrospray sample-introduction system. This instrument system was used to obtain LC/mass spectrometry (MS) data from the commercially available cyanobacteria toxins (microcystin-LR, -YR, -RR and nodularin). We review the electrospray mass spectra of these toxins and the significance of accurate m/z measurements of toxin precursor and product ions. We discuss the collision-induced dissociation of [M + H]+, [M + H]2+, and fragment ions in terms of ion-fragmentation pathways and mechanisms. The principal focus of this review is the potential for the efficient determination of microcystin structures with these MS techniques when no analytical standards are available or when new microcystin toxins are present in a sample.