Palytoxin is a potent marine toxin and one of the most complex natural compounds ever described. A number of compounds identified as palytoxin congeners (e.g., ovatoxins, mascarenotoxins, ostreocins, etc.) have not been yet structurally elucidated due to lack of pure material in quantities sufficient to an NMR-based structural investigation. In this study, the complex fragmentation pattern of palytoxin in its positive high resolution liquid chromatography tandem mass spectra (HR LC-MS(n)) was interpreted. Under the used conditions, the molecule underwent fragmentation at many sites of its backbone, and a large number of diagnostic fragment ions were identified. The natural product itself was used with no need for derivatization. Interestingly, most of the fragments contained calcium in their elemental formula. Evidence for palytoxin tendency to form adduct ions with calcium and other divalent cations in its mass spectra was obtained. Fragmentation pattern of palytoxin was used as template to gain detailed structural information on ovatoxin-a, the main toxin produced by Ostreopsis ovata, (observe correct font) a benthic dinoflagellate that currently represents the major harmful algal bloom threat in the Mediterranean area. Either the regions or the specific sites where ovatoxin-a and palytoxin structurally differ have been identified.