Kingdom Protoctista Hogg, 1860
   1.1 Phylum Rhizopoda Dujardin, 1835 - rhizopods see Phylum Cercozoa Cavalier-Smith, 1998
   1.2 Phylum Haplosporidia Caullery & Mesnil, 1899 see Order Haplosporida M. Caullery & F. Mesnil, 1899
   1.3 Phylum? Paramyxea Levine, in Sprague, 1979 see Phylum Paramyxa
   1.4 Phylum Myxozoa Grassé, 1970, incertae sedis - myxozoans see Subphylum Myxozoa Grassé, 1970
   1.5 Phylum Microspora Sprague, 1977 - microsporans see Phylum Microsporida Balbiani, 1882
   2.1 Phylum Acrasea Olive, 1975 see Class Mycetozoa de Bary, 1859
   2.2 Phylum Dictyostelida see Order Dictyosteliida L. Olive, 1970
   2.3 Phylum Rhodophyta Wettst. (1901) - red algae
   2.4 Phylum Conjugaphyta see Phylum Chlorophycota
   3.01 Phylum Xenophyophora Schulze, 1904
   3.02 Phylum Cryptophyta Caval.-Sm. (1986) - cryptomonads see Superclass Cryptomonada Cavalier-Smith, 2004
   3.03 Phylum Glaucocystophyta Kies & Kremer (1986) see Phylum Glaucophyta Skuja (1954)
   3.04 Phylum Karyoblastea Margulis, 1974
   3.05 Phylum Zoomastigina see Phylum Discomitochondria
   3.06 Phylum Euglenida Bütschli, 1884
   3.07 Phylum Chlorarachnida Hibberd & Norris, 1984 see Order Chlorarachnida Hibberd & Norris, 1984
   3.08 Phylum Prymnesiophyta Hibberd (1976), nom. inval. - haptophytes see Phylum Prymnesiophyta Hibberd ex Doweld (2001)
   3.09 Phylum Raphidophyta see Phylum Ochrophyta Caval.-Sm. (1995)
   3.10 Phylum Eustigmatophyta Hibberd & Leedale (1970) see Phylum Ochrophyta Caval.-Sm. (1995)
   3.11 Phylum Actinopoda Calkins, 1902
   3.12 Phylum Hyphochytriomycota Whittaker (1969), nom. inval. see Phylum Hyphochytriomycota Margulis ex Doweld (2001)
   3.13 Phylum Labyrinthulomycota F.C. Page (1980)
   3.14 Phylum Plasmodiophoromycota Whittaker (1969), nom. nud. see Phylum Plasmodiophoromycota Doweld (2001)
   4.01 Phylum Dinoflagellata Engl. (1903) see Superclass Dinoflagellata Bütschli, 1885
   4.01.0 Phylum Dinomastigota Margulis, 1996 see Phylum Dinoflagellata Engl. (1903)
   4.02 Phylum Chrysophyta Pascher (1914) see Class Chrysophyceae Fritsch (1927)
   4.03 Phylum Chytridiomycota Arx (1967), nom. inval. see Phylum Chytridiomycota Doweld (2001)
   4.04 Phylum plasmodial slime molds see Class Mycetozoa de Bary, 1859
   4.05 Phylum Ciliophora Doflein, 1901 - ciliates
   4.06 Phylum Granuloreticulosa de Saedeleer, 1934 see Phylum Foraminifera d'Orbigny, 1826
   4.07 Phylum Apicomplexa Levine, 1970 see Infraphylum Apicomplexa Levine, 1970
   4.08 Phylum Bacillariophyta Engl. & Gilg (1919) - diatoms see [unranked] Diatomea Kütz. (1844)
   4.09 Phylum Chlorophyta Pascher (1914) - green algae
   4.10 Phylum Oomycota Arx (1967)
   4.11 Phylum Xanthophyta Allorge, in Fritsch (1935) see Class Xanthophyceae P. Allorge ex Fritsch (1935)
   4.12 Phylum Phaeophyta Kjellman (1891) see Phylum Phaeophycota
   5.1 Ellobiopsida Whisler, 1990, incertae sedis
   5.1.0 Class ellobiopsids incertae sedis
   5.2 ebridians incertae sedis see Class ebriids
   5.2.0 Class ebriids incertae sedis see [unranked] ebriids