Sphaerodinium cracoviense was collected near Cracow, Poland, and analysed by light microscopy, scanning electron microscopy, and serial-section transmission electron microscopy. Thecae showed a peridinioid type of plate arrangement with unusual numbers in the anterior intercalary and postcingular plate series: 4 and 6, respectively. The apical pore of S. cracoviense differed from the typical arrangement seen in many thecate forms and included a furrow with knob-like protuberances reminiscent of the apical area of some woloszynskioids. The flagellar apparatus included the three microtubular roots that extend to the left of the basal bodies and a striated root connective between the transverse striated root and the longitudinal microtubular root. Both the single-stranded root that associates with the right side of the longitudinal basal body in peridinioids and gonyaulacoids, and the layered connective typical of peridinioids were absent. The eyespot was formed by a layer of vesicle-contained crystal-like units underlain by layers of variably fused globules not bounded by membranes, and represents a novel type. The pusular system included a long canal with a dilated inner portion with radiating tubules. Bayesian and maximum likelihood analyses based on large subunit rDNA placed Sphaerodinium as a sister taxon to a group of woloszynskioids and relatively far from Peridinium and its allies