Investigation of phytoplankton from East China Sea of the Pacific Ocean, offshore Réunion Island of the Indian Ocean, and the French Atlantic coast revealed a species of poorly known armored fusiform dinoflagellate. To clarify this species, morphology and phylogeny based on mitochondrial and nuclear protein gene sequence (Cox1, Cob and Hsp90) concatenated with the SSU, ITS region and LSU rDNA sequences were analysed. Epifluorescence and scanning electron microscopy observations revealed that the nucleus of the specimen was elongated, sausage-shaped and located equatorially on the left lateral side of the cell, and that the plate formula is Po, 3′, 1a, 6″, 6C, 8S, 5‴, 1p, 2′‴. These morphological features indicate that the species can be assigned to Centrodinium punctatum. Interestingly, the phylogenetic analyses placed this species within the Alexandrium clade, with Alexandrium affine being its closest relative. This indicates that genus Alexandrium is not monophyletic. The most similar morphological traits between C. punctatum and Alexandrium species were the shape of apical pore plate and the arrangement of the sulcal plates. However, since there are significant morphological differences between C. punctatum and Alexandrium species, further studies are needed to clarify the relation between the morphology and molecular phylogeny of other Centrodinium-related fusiform species.