The benthic dinoflagellate Gambierdiscus is regarded as the primary causative agent of Ciguatera Fish Poisoning (CFP), a disease prevalent in the Pacific regions, the Carribean and the Indian Ocean. Six distinct species within this genus, most of them being toxic, have been described so far on the basis of morphological criteria. The genetic characterization of various strains of G. toxicus has also been addressed in recent studies. In the present work, we investigated the usefulness of the rRNA genes for the molecular characterization and classification of 15 clones of Gambierdiscus distributed in 5 of the 6 species described to date. The 5.8S+ITS and the LSU rDNA D8-D10 regions of 11 Polynesian isolates were PCR-amplified prior to their cloning and sequencing, for phylogenetic analysis by means of sequence comparison. Both regions proved to be useful biogeographical markers, as a grouping of these isolates according to their geographic origin was globally observed. To investigate the potential interest of the LSU rDNA D8-D10 regions in Gambierdiscus systematics, sequences of 8 isolates from distinct geographic origins, distributed among the morphospecies G. toxicus, G. yasumotoi, G. polynesiensis, G. australes and G. pacificus, were also compared. Four molecular types could be distinguished, which tend to indicate that species designations in this genus based on SEM microscopy are consistent with classification inferred from genetic heterogeneities. The relevance of a modern form of taxonomy in dinoflagellates that would combine both molecular and traditional morphological criteria, is also discussed.