They are distinguished by having their two flagella inserted apically, rather than ventrally as in other groups.

One flagellum extends forward and the other circles its base, and there are no flagellar grooves.

Accordingly, the Prorocentrales may be called desmoflagellates, and in some classifications were treated as a separate class Desmophyceae.

All members have chloroplasts and a theca, which is composed of two large plates joined by a sagittal suture.

This structure is shared with the Dinophysiales, and they are probably sister groups.