This study maps the targeted metabolite fingerprints of thirteen Gambierdiscus, five Coolia, and two Fukuyoa species, analyzing 34 isolates. The metabolite profiles were assessed using targeted LC-MS/MS analysis of 56 characterized secondary metabolites. Gambierdiscus polynesiensis was the only species to produce several Pacific ciguatoxins (P-CTXs), including P-CTX3B, P-CTX3C, iso-P-CTX3B/C, P-CTX4A, P-CTX4B, and iso-P-CTX4A/B. G. australes produced maitotoxins (MTXs) MTX-1 and MTX-5, while G. cheloniae produced MTX-6 and G. honu produced MTX-7. All Gambierdiscus isolates produced 44-methylgambierone (44-MG), with nine species also producing gambierone. Additional gambierone analogues, including anhydrogambierone, were detected in all Gambierdiscus species, two Coolia, and two Fukuyoa species. Gambieroxide was detected in G. lewisii and G. pacificus, while gambieric acid A was detected in ten Gambierdiscus species, with G. australes (CAWD381) being the only isolate to produce gambieric acids A–D. The study highlights several species producing 'unknown' compounds with characteristics of cyclic polyethers, which will be the focus of future compound discovery efforts. The results show that the isolates tested produce known CTXs or MTXs, but not both, and emphasize the need to identify both known and unknown compounds to understand their role in ciguatera poisoning (CP) and potential risks to human health. The study also demonstrates the importance of understanding the metabolic diversity of these species to better assess their impact on marine ecosystems and human health.This study maps the targeted metabolite fingerprints of thirteen Gambierdiscus, five Coolia, and two Fukuyoa species, analyzing 34 isolates. The metabolite profiles were assessed using targeted LC-MS/MS analysis of 56 characterized secondary metabolites. Gambierdiscus polynesiensis was the only species to produce several Pacific ciguatoxins (P-CTXs), including P-CTX3B, P-CTX3C, iso-P-CTX3B/C, P-CTX4A, P-CTX4B, and iso-P-CTX4A/B. G. australes produced maitotoxins (MTXs) MTX-1 and MTX-5, while G. cheloniae produced MTX-6 and G. honu produced MTX-7. All Gambierdiscus isolates produced 44-methylgambierone (44-MG), with nine species also producing gambierone. Additional gambierone analogues, including anhydrogambierone, were detected in all Gambierdiscus species, two Coolia, and two Fukuyoa species. Gambieroxide was detected in G. lewisii and G. pacificus, while gambieric acid A was detected in ten Gambierdiscus species, with G. australes (CAWD381) being the only isolate to produce gambieric acids A–D. The study highlights several species producing 'unknown' compounds with characteristics of cyclic polyethers, which will be the focus of future compound discovery efforts. The results show that the isolates tested produce known CTXs or MTXs, but not both, and emphasize the need to identify both known and unknown compounds to understand their role in ciguatera poisoning (CP) and potential risks to human health. The study also demonstrates the importance of understanding the metabolic diversity of these species to better assess their impact on marine ecosystems and human health.