Several cultured strains of Gymnodinium catenatum isolated worldwide have been shown to produce important proportions of the recently discovered benzoate paralytic shellfish poisoning (PSP) toxins GC1 through GC3. These toxins pose a new challenge for the HPLC analysis of shellfish predating during blooms of this microalga because due to their hydrophobicity are retained along the C18 solid-phase extraction step employed to eliminate interferences. The production of GC toxins was confirmed in a clone of G.catenatum isolated from the Portuguese Northwest coast during the winter bloom of 2005, in addition to a clone from 1989 reported previously by other authors. The major peroxide oxidation products of GC1+2 and GC3 were, respectively, dcGTX2+3 and dcSTX. The search of benzoate analogues in bivalves contaminated during the winter 2005 bloom showed these analogues constituted a minor component of the N(1)-H containing toxins, as selectively detected by peroxide oxidation. While in G.catenatum GC1-3 were the major components after C1+2 and B1, in bivalves dcGTX2+3 and dcSTX were the major components after C1+2 and B1. Similar conclusions were later extended to more shellfish species naturally contaminated during the autumn bloom of 2007. In the gut content of sardines GC toxins were present, while in crabs predating upon shellfish, these were absent. A generalised conversion of GC toxins into decarbamoyl analogues was confirmed by in vitro incubations of bivalve's digestive glands with semi-purified GC toxins. This is the first report of widespread carbamoylase activity in shellfish, exclusively targeted at benzoate PSP analogues and that is heat-inactivated. Despite the high proportion of benzoate analogues produced by G.catenatum, analyses of bivalves contaminated with PSP toxins seem to be simplified due to the important conversion of benzoate into decarbamoyl analogues that occurs in bivalves. These last analogues are detected by common HPLC methods used for food protection.