分子系統学
Molecular phylogenetics show that dinoflagellates are grouped with ciliates and apicomplexans (=Sporozoa) in a well-supported clade, the alveolates. The closest relatives to dinokaryotic dinoflagellates appear to be apicomplexans, "Perkinsus, Parvilucifera", syndinians, and "Oxyrrhis". Molecular phylogenies are similar to phylogenies based on morphology.