Several populations of Peridinium lomnickii were examined by SEM and serial section TEM. Comparison with typical Peridinium, Peridiniopsis, Palatinus and Scrippsiella species revealed significant structural differences, congruent with phylogenetic hypotheses derived from partial LSU rDNA sequences. Chimonodinium gen. nov. is described as a new genus of peridinioids, characterized by the Kofoidian plate formula Po, cp, x, 4', 3a, 7'', 6c, 5s, 5''', 2'''', the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle, a pusular system with well-defined pusular tubes connected to the flagellar canals, and the production of non-calcareous cysts. Serial section examination of Scrippsiella trochoidea, here taken to represent typical Scrippsiella characters, revealed no peduncle and no associated microtubular strands. The molecular phylogeny placed C. lomnickii comb. nov. as a sister group to a clade composed of Thoracosphaera and the pfiesteriaceans. Whereas the lack of information on fine structure of the swimming stage of Thoracosphaera leaves its affinities unexplained, C. lomnickii shares with the pfiesteriaceans the presence of a microtubular basket and the unusual connection between two plates on the left side of the sulcus, involving extra-cytoplasmic fibres.