A naked dinoflagellate producing microreticulate cysts is described as Gymnodinium nolleri sp. nov. It was previously misidentified as Gymnodinium catenatum based on strong morphological similarity with this species in both the cyst and motile stages. Gymnodinium nolleri differs from G. catenatum primarily in the size of the cyst and the Vegetative stage, G. nolleri being smaller although there is overlap, particularly in the size of the vegetative cell. The cyst of G. nolleri is 28-38 mu m in diameter, whereas G. catenatum measures 38-59 mu m. The vegetative cell of G. nolleri on average is 26 x 33 mu m and G. catenatum is 36 x 45 mu m. The motile stage of G. nolleri never forms long chains, whereas such chains are common in G. catenatum. The cyst of G. nolleri has fewer rows of polygons in the paracingulum than G. catenatum, and the polygons on the cyst are generally slightly smaller, although they appear larger due to the smaller size of the cyst. These differences and earlier described differences at the molecular level (large subunit ribosomal RNA sequence, isozyme profile, lack of paralytic shellfish poisoning (PSP) toxins in G. nolleri) justify describing G. nolleri as a new species. The fine structure of the flagellar apparatus of G. nolleri is included in the description. It shows features common to most dinoflagellates studied so far and has many similarities with the flagellar apparatus of 'Gymnodinium sp.' of Roberts (1986) and G. catenatum, e.g. a nuclear fibrous connective, longitudinal microtubular root-longitudinal basal body connectives, and a longitudinal microtubular root-ventral ridge connective.