They include all species where the nucleus remains a dinokaryon throughout the entire cell cycle, which is typically dominated by the haploid stage.

Species with a theca are divided into four orders, based on the arrangement of the armor plates: The Peridiniales are probably paraphyletic to the others, and on rRNA trees they are mixed with the species that lack thecae.

The other three orders are probably monophyletic, with the Dinophysiales and Prorocentrales as close relatives, united by the presence of a sagittal suture dividing the theca in two.

[3] The groups of dinoflagellates without theca are understood to be artificial, and are mostly polyphyletic.

There is also a group of parasitic dinoflagellates, the Blastodiniales, that do not have dinokarya during their trophic stage.