The genus Prorocentrum is diverse and comprises mostly marine dinoflagellates with a worldwide distribution. One large, common and easily recognizable planktonic species of Prorocentrum was known for a long time as P. compressum. This name, however, is incorrectly linked to a basionym of a diatom. The confusing taxonomy of the now also lectotypified diatom name was recently resolved, and the next younger available name, Prorocentrum bidens, was proposed for the dinoflagellate species. Based on multiple strains from various localities we here provide the first detailed morphological study of P. bidens thereby propagating the correct nomenclature of this species. The cells of one strain differed consistently from material assigned to P. bidens, and Prorocentrum bisaeptum sp. nov. is described here to represent this closely related species. Both species possessed two pyrenoids per chloroplast and shared the arrangement of ten periflagellar platelets, including subdivisions of platelets 6 and 8. Cells of both species were either fully motile or, in an encapsulated stage, enclosed with actively beating flagella in a hyaline flexible envelope bounded by a thin surface layer. Prorocentrum bisaeptum differs from P. bidens by a more elongated shape of the cells and by a smooth (not foveate) surface of the thecal plates. Most importantly, one to four cells of P. bisaeptum are consistently enclosed within two nesting envelopes, whereas there is only one such structure tightly surrounding one or two cells of P. bidens. This study increases and improves our knowledge of the diversity within this important group of planktonic organisms.