This study mapped the metabolite fingerprint of 34 isolates from thirteen *Gambierdiscus*, five *Coolia*, and two *Fukuyoa* species using targeted LC–MS/MS analysis. The isolates were assessed for the production of 56 characterized secondary metabolites, including ciguatoxins (CTXs), maitotoxins (MTXs), and gambierones. *Gambierdiscus polynesiensis* was the only species to produce CTXs, while *G. australis* produced MTX-1 and MTX-5. *G. chelonie* produced MTX-6, and *G. honu* produced MTX-7. Ubiquitous production of 44-methylgambierone was observed among all *Gambierdiscus* isolates, with nine species also producing gambierone. Additional gambierone analogues, including anhydrogambierone, were detected in all *Gambierdiscus* species, two *Coolia* species, and two *Fukuyoa* species. Gambiroxide was detected in *G. levisii* and *G. pacificus*, and gambieric acid A was detected in ten *Gambierdiscus* species. This study highlights the production of 'unknown' compounds by several species, which will be the focus of future compound discovery efforts. The results also demonstrate that the isolates produce known CTXs or MTXs but not both, and that the distribution of *G. polynesiensis* does not align with global intoxication events.This study mapped the metabolite fingerprint of 34 isolates from thirteen *Gambierdiscus*, five *Coolia*, and two *Fukuyoa* species using targeted LC–MS/MS analysis. The isolates were assessed for the production of 56 characterized secondary metabolites, including ciguatoxins (CTXs), maitotoxins (MTXs), and gambierones. *Gambierdiscus polynesiensis* was the only species to produce CTXs, while *G. australis* produced MTX-1 and MTX-5. *G. chelonie* produced MTX-6, and *G. honu* produced MTX-7. Ubiquitous production of 44-methylgambierone was observed among all *Gambierdiscus* isolates, with nine species also producing gambierone. Additional gambierone analogues, including anhydrogambierone, were detected in all *Gambierdiscus* species, two *Coolia* species, and two *Fukuyoa* species. Gambiroxide was detected in *G. levisii* and *G. pacificus*, and gambieric acid A was detected in ten *Gambierdiscus* species. This study highlights the production of 'unknown' compounds by several species, which will be the focus of future compound discovery efforts. The results also demonstrate that the isolates produce known CTXs or MTXs but not both, and that the distribution of *G. polynesiensis* does not align with global intoxication events.