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:
- Gymnodiniphycidae
- Gymnodiniales
- Ptychodiscales
- Suessiales
- Peridiniphycidae
- Peridiniales
- Gonyaulacales
- Dinophysiphycidae: Dinophysiales
- Prorocentrophycidae: Prorocentrales
- Incertae sedis
- Desmocapsales
- Phytodiniales (or Dinococcales, includes Dinotrichales)
- Thoracosphaerales