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The genus <i>Gambierdiscus</i> produces an array of bioactive hydrophilic and lipophilic secondary metabolites that range in mode of action and toxicity. In this study, the metabolite fingerprint was mapped for thirteen <i>Gambierdiscus</i>, five <i>Coolia</i> and two <i>Fukuyoa</i> species (34 isolates) by assessing the production of 56 characterised secondary metabolites. <i>Gambierdiscus polynesiensis</i> was the only species to produce Pacific-ciguatoxin-3B (P-CTX3B), P-CTX3C, iso-P-CTX3B/C, P-CTX4A, P-CTX4B and iso-P-CTX4A/B. <i>G. australes</i> produced maitotoxin-1 (MTX-1) and MTX-5, <i>G. cheloniae</i> produced MTX-6 and <i>G. honu</i> produced MTX-7. Ubiquitous production of 44-methylgambierone was observed amongst all the <i>Gambierdiscus</i> isolates, with nine species also producing gambierone. Additional gambierone analogues, including anhydrogambierone (tentatively described herein), were also detected in all <i>Gambierdiscus</i> species, two <i>Coolia</i> and two <i>Fukuyoa</i> species. Gambieroxide was detected in <i>G. lewisii</i> and <i>G. pacificus</i> and gambieric acid A was detected in ten <i>Gambierdiscus</i> species, with <i>G. australes</i> (CAWD381) being the only isolate to produce gambieric acids A–D. This study has demonstrated that the isolates tested to date produce the known CTXs or MTXs, but not both, and highlighted several species that produced ‘unknown’ compounds displaying characteristics of cyclic polyethers, which will be the focus of future compound discovery efforts.