The classification of Ceratophyllales has long been problematic. The family has been placed near Magnoliidae or Monocots. In the Apg3 classification Ceratophyllales is been placed at the beginning of the Dicotylodons or Eudicotyledons. Eudicotyledons are the Fabanae, Malvanae and Asteranae. They are all the Angiospermae without the Amborellanae, Magnolianae and Lilianae. Ceratophyllales was considered relative of Nymphaeaceae and included in Nymphaeales in the Cronquist system.
In the Plant theory the Ceratophyllidae are a Subclass of the Fabanae. They have the emphasis on the Hydrogen series. Ceratophyllidae is a new name used to notify that it is a Subclass of the Fabanae in the Plant theory.
The Ceratophyllidae have one Order, Ceratophyllales and one Family, Ceratophyllaceae.