3 Sako, Y. Yagi, M. Chinain, M. Legrand, A-M. Nakahara, H. Kurokawa, T. S. Uchida, A. Ishida, Y. Inoue, A. 1996 In: Harmful and toxic algal blooms, Yasumoto T, Oshima Y, Fukuyo Y (Eds), Intergovernmental Oceanographic Commission of UNESCO, pp 443-446 1996 To analyze the molecular phylogeny of ciguatera-causing dinoflagellate Gambierdiscus toxicus Adachi et Fukuyo, as a first step we established the method of extraction and purification of total DNA. Cell grinding in liquid nitrogen was the best way for extracting total DNA from G. toxicus, and further purification of DNA with cetyltrimethylammonium bromide (CTAB) was essential for polymerase chain reaction (PCR).The 18S ribosomal DNA(18S rDNA) from seven isolates of G. toxicus from French Polynesia, Japan and the West Indies were amplified by PCR and partially sequenced to investigate phylogenetic relationship within Dinophyceae. Phylogeny inferred from the sequence comparison revealed the specific phylogenetic position of the genus Gambierdiscus. The genetic distance values between isolates of G. toxicus and other five species of dinoflagellate were quite high, although distance values within isolates of G. toxicus were very low except for one isolate from the West Indies. Partial sequence analysis of 18S rDNA could not discriminate the population of G. toxicus, but the 5.8S rDNA and flanking internal transcribed spacer (ITSs) regions had a possibility to discriminate intraspecific difference.