Phylum Dinoflagellata Engl. (1903) see Superclass Dinoflagellata Bütschli, 1885
   Subphylum Dinokaryota Fensome, F.J.R. Taylor, G. Norris, Sarjeant, Wharton & G.L. Williams (1993)
     Class Dinophyceae Pascher (1914)
       01 Subclass Gymnodiniphycidae Fensome, F.J.R. Taylor, G. Norris, Sarjeant, Wharton & G.L. Williams (1993)
       02 Subclass Peridiniphycidae Fensome, F.J.R. Taylor, G. Norris, Sarjeant, Wharton & G.L. Williams (1993)
       03 Subclass Dinophysiphycidae Möhn ex Fensome, F.J.R. Taylor, G. Norris, Sarjeant, Wharton & G.L. Williams (1993)
       04 Subclass Prorocentrophycidae Fensome, F.J.R. Taylor, G. Norris, Sarjeant, Wharton & G.L. Williams (1993) [monotypic]
       05 Genus Moestrupia Gert Hansen & Daugbjerg (2011), incertae sedis
       06 Order Desmocapsales Pascher (1914), incertae sedis [monotypic]
       07 Order Phytodiniales T. Christ. ex A.R. Loebl. (1970), incertae sedis see Order Dinococcales Pascher (1914)
       08 Order Thoracosphaerales Tangen (1982), incertae sedis [monotypic] see Order Peridiniales Haeckel (1894)
       09 Genus †Cobricosphaeridium Harland & Sarjeant (1970), incertae sedis
       10 Genus †Diacrocanthidium Deflandre & Foucher (1967), incertae sedis
       11 Genus †Prolixosphaeridium Davey, Downie, Sarjeant & Williams (1966), incertae sedis
       12 Genus Pileidinium M. Tamura & T. Horig. (2005), incertae sedis
       13 Genus Pseliodinium Sournia (1972), incertae sedis
       14 Genus Pyramidodinium T. Horig. & C. Sukigara (2005), incertae sedis
       15 Genus †Suibindia Jingxian Yu (1982), incertae sedis
       16 Genus Tintinnophagus Coats (2010), incertae sedis
       17 Genus †Xylochoarion Erkmen & Sarjeant (1978), incertae sedis
       18 Genus Zoorhabdella Rhumbler (1909), incertae sedis
       19 Genus Zooxanthella K. Brandt (1881), incertae sedis