The Dinophyceae are the main class of dinoflagellates, excluding only a few peculiar groups that appear to have diverged from the others early on. They include all forms where the nucleus is dinokaryotic throughout the entire life cycle, which is typically haploidal. Fensome et al. recognise the following subclasses and orders:

• Subclass Gymnodiniphycidae
  • Gymnodiniales
  • Ptychodiscales
  • Suessiales
• Subclass Peridiniphycidae
  • Peridiniales
  • Gonyaulacales
• Subclass Dinophysiphycidae
  • Dinophysiales
• Subclass Prorocentrophycidae
  • Prorocentrales
• uncertain classification:
  • Desmocapsales
  • Phytodiniales (or Dinococcales, includes Dinotrichales)
  • Thoracosphaerales

The Blastodiniales , a small group of parasitic forms with temporary dinokaryotes, appear to belong here as well though they were treated as a separate class. Earlier schemes have also separated out the Prorocentrales, which have apical rather than lateral flagella, as the class Desmophyceae. However, nearly all of these orders appear to be polyphyletic, and the same applies even to several well-known genera such as Gymnodinium and Peridinium .