Dinoflagellates of the genus Dinophysis are agents of Diarrhoeic Shellfish Poisoning (DSP) and are one of the main risk factors affecting shellfish exploitation in the Iberian Peninsula and Europe. Not much has been learned about the biochemistry, genetics and ecology of these algae because they are notoriously difficult to culture and remain largely recalcitrant to most contemporaneous protocols routinely used with other microbes. Also the methodologies for their detection and identification in natural habitats need to be improved. Both aspects are interrelated since for instance as better knowledge of their genetic will help to develop better methods of detection, and better methods of detections would help the study of their physiology and ecology. At present, rapid progress of knowledge of these species at the molecular and biochemical levels is dependent on technological innovations. Although, some techniques can be directly translated from existing protocols, many of them will require extensive modification. For some molecular biology applications, the preparation of clean DNA is required, however the existing protocols for this purpose need to start with a high amounts of cells. This is particularly difficult to achieve in the case of Dinophysis species since cells have to be manually collected from the sea samples. We will present a methodology that allow the obtention of clean enough DNA for molecular biology applications using just a few cells.