Domoic acid (DA) was first detected in France in mussel flesh in 1998, outbreak that was linked to the presence of Pseudo-nitzschia pseudodelicatissima. Ever since, the phytoplankton monitoring program (REPHY, Réseau de surveillance du Phytoplancton et des Phycotoxines) also monitors DA content in shellfish flesh. Amnesic shellfish poisoning (ASP) has been recurrently detected, and was over the sanitary threshold in the years 2000 and 2004 in Brittany and in 2002 in the Mediterranean coast (Amzil, 2001; Amzil pers. comm.). Toxicity events are usually dominated by several Pseudo-nitzschia species, although different strains might be or not be toxic (Bates et al., 1998). This is why an inventory of the species present in the French coasts and their molecular characterisation needed to be carried out. A methodology to get Pseudo-nitzschia DNA directly from natural samples fixed with lugol is presented. The DNA sequences obtained in this study will be use to produce specific molecular markers of Pseudo-nitzschia species.