The taxonomic position of Blastodinium navicula Chatton and B. contortum Chatton, parasites of marine copepods, was investigated on the basis of morphological observations and molecular data. The life cycle of Blastodinium includes a parasitic stage, a trophont, and free-swimming dinospores. The individual cells in the trophont, as well as the dinospores that they produced, were thecate. Dinospores of B. contortum and B. navicula had peridinioid plate tabulation formula, demonstrating an affiliation to the order Peridiniales Heackel (subdivision Dinokaryota Fensome et al.). This systematic position is in contrast to current classifications, in which the order Blastodiniales Chatton is thought to represent an early evolutionary branch of the dinokaryote lineage. Small-subunit rRNA gene sequences were generated from six Blastodinium individuals isolated from three different host species. In phylogenetic analyses based on SSU rRNA genes, Blastodinium spp. branched with the typical dinoflagellates. Even though overall statistical support was low, the analyses suggested that Blastodinium spp. are late-branching, dinokaryote dinoflagellates. Species currently included in Blastodiniales are all parasites, but they are morphologically and functionally diverse. Emerging molecular data also reveal high genetic diversity, and therefore, the taxonomy of the group requires reevaluation.