To determine the intraspecific variability of microscopic organisms such as dinophytes is challenging, but can be achieved using cultured material. Unusual morphologies of Peridinium tuberosum assigned to the Peridinium cinctum species group have been described as bulges on the posterior end of the cell a hundred years ago and more, but its taxonomic significance is unclear at present. We collected field material in Germany and Poland in order to establish strains to study cell morphology using light and scanning electron microscopy. For the cultured material, DNA sequence data from the rRNA operon was gained as well and included in molecular phylogenetics (including 22 new partial rRNA sequences). Two new, closely related ribotypes were detected, and all strains showed the principle morphology of P. cinctum having an asymmetric epitheca, a large first apical plate and a sulcus extending onto the epitheca. In the single-strain GeoM*979 assigned to one of the two new ribotypes, cells with bulges appeared rarely but consistently, mostly on the hypotheca, but other variations also occurred. Overall, cells of this strain display traits not observed before while studying cultured P. cinctum, and this distinction is further supported by molecular data and additional details of epithecal opening. However, there does not remain enough information to determine strain GeoM*979 as a separate species (namely P. tuberosum) and therefore, it is identified as Peridinium aff. cinctum until further notice.