Abeoforma Marshall & Berbee, 2011 (verified source for family)
Acanthoecida (additional source)
Acanthoecidae Norris, 1965 (additional source)
Amoebidiales accepted as Eccrinida (source of synonymy)
Amoeboaphelidiidae Cavalier-Smith, 2013 accepted as Aphelidiaceae L. Tedersoo, S. Sanchez-Ramirez, U. Kõljalg, M. Bahram, M. Döring, D. Schigel, T.W. May, M. Ryberg & K. Abarenkov, 2018 (basis of record)
Amoeboaphelidiidae Cavalier-Smith, 2013 accepted as Aphelidiaceae L. Tedersoo, S. Sanchez-Ramirez, U. Kõljalg, M. Bahram, M. Döring, D. Schigel, T.W. May, M. Ryberg & K. Abarenkov, 2018 (original description)
Amoeboaphelidiidae Cavalier-Smith, 2013 accepted as Aphelidiaceae L. Tedersoo, S. Sanchez-Ramirez, U. Kõljalg, M. Bahram, M. Döring, D. Schigel, T.W. May, M. Ryberg & K. Abarenkov, 2018 (taxonomy source)
Amoeboaphelidiidae Cavalier-Smith, 2013 accepted as Aphelidiaceae L. Tedersoo, S. Sanchez-Ramirez, U. Kõljalg, M. Bahram, M. Döring, D. Schigel, T.W. May, M. Ryberg & K. Abarenkov, 2018 (extant flag source)
Amphibiocystidium Pascolini, Daszak, Cunningham, Tei, Vagnetti, Bucci, Fagotti & Di Rosa, 2003 (verified source for family)
Amphibiothecum Feldman, Wimsatt & Green, 2005 accepted as Dermocystidium Pérez, 1908 (verified source for family)
Anaeromonadea (additional source)
Anaeromonadea (taxonomy source)
Ancyromonadidae Cavalier-Smith, 1993 (basis of record)
Ancyromonadidae Cavalier-Smith, 1993 (taxonomy source)
Ancyromonadidae Cavalier-Smith, 1993 (current name source)
Ancyromonadidae Cavalier-Smith, 1993 (extant flag source)
Ancyromonas W.S. Kent, 1880 (verified source for family)
Andalucia Lara, Chatzinotas & Simpson, 2006 (verified source for family)
Andaluciidae Cavalier-Smith, 2013 (taxonomy source)
Andaluciidae Cavalier-Smith, 2013 (current name source)
Andaluciidae Cavalier-Smith, 2013 (extant flag source)
Andaluciidae Cavalier-Smith, 2013 (basis of record)
Andaluciidae Cavalier-Smith, 2013 (original description)
Anurofeca Baker, Beebee & Ragan, 1999 (verified source for family)
Apusomonadida (taxonomy source)
Apusomonadida (additional source)
Apusomonadida (extant flag source)
Apusozoa (additional source)
Apusozoa (taxonomy source)
Apusozoa (extant flag source)
Breviata Walker, Dacks & Embley, 2006 (verified source for family)
Breviatea (additional source)
Breviatea (taxonomy source)
Breviatida (basis of record)
Breviatida (taxonomy source)
Breviatida (extant flag source)
Breviatidae Cavalier-Smith, 2013 (taxonomy source)
Breviatidae Cavalier-Smith, 2013 (extant flag source)
Breviatidae Cavalier-Smith, 2013 (basis of record)
Breviatidae Cavalier-Smith, 2013 (original description)
Breviatidae Cavalier-Smith, 2013 (current name source)
Brugerolleia Desser, Hong, Siddall & Barta, 1993 (verified source for family)
Calonymphidae Grassi, 1911 (taxonomy source)
Calonymphidae Grassi, 1911 (additional source)
Calonymphidae Grassi, 1911 (current name source)
Capsaspora Hertel, Bayne & Loker, 2002 (verified source for family)
Capsaspora Hertel, Bayne & Loker, 2002 (current name source)
Capsasporidae Cavalier-Smith, 2008 (basis of record)
Capsasporidae Cavalier-Smith, 2008 (taxonomy source)
Capsasporidae Cavalier-Smith, 2008 (current name source)
Capsasporidae Cavalier-Smith, 2008 (extant flag source)
Carpediemonadea accepted as Carpomonadea (source of synonymy)
Carpediemonadida (additional source)
Carpediemonadida (taxonomy source)
Carpediemonadida (extant flag source)
Carpediemonadidae Cavalier-Smith, 2003 (current name source)
Carpediemonadidae Cavalier-Smith, 2003 (additional source)
Carpediemonadidae Cavalier-Smith, 2003 (taxonomy source)
Carpomonadea (taxonomy source)
Carpomonadea (original description)
Caviomonadidae Cavalier-Smith, 2013 (extant flag source)
Caviomonadidae Cavalier-Smith, 2013 (original description)
Caviomonadidae Cavalier-Smith, 2013 (current name source)
Caviomonadidae Cavalier-Smith, 2013 (basis of record)
Caviomonadidae Cavalier-Smith, 2013 (taxonomy source)
Caviomonas Nie, 1950 (verified source for family)
Chilomastigida (taxonomy source)
Chilomastigida (basis of record)
Chilomastigida (original description)
Chilomastigida (extant flag source)
Chilomastigida (habitat flag source)
Chilomastigidae Cavalier-Smith, 2013 (basis of record)
Chilomastigidae Cavalier-Smith, 2013 (original description)
Chilomastigidae Cavalier-Smith, 2013 (extant flag source)
Chilomastigidae Cavalier-Smith, 2013 (habitat flag source)
Chilomastigidae Cavalier-Smith, 2013 (taxonomy source)
Chilomastigidae Cavalier-Smith, 2013 (current name source)
Choanofila (additional source)
Choanofila (taxonomy source)
Choanofila (extant flag source)
Choanoflagellatea (taxonomy source)
Choanoflagellatea (additional source)
Choanozoa (taxonomy source)
Choanozoa (additional source)
Choanozoa (extant flag source)
Cochlosomatidae Tyzzer, 1930 accepted as Trichomonadidae Chalmers & Pekkoloa, 1918 (source of synonymy)
Corallochytrea (additional source)
Corallochytrea (taxonomy source)
Corallochytrida (basis of record)
Corallochytrida (taxonomy source)
Corallochytrida (extant flag source)
Corallochytriidae Cavalier-Smith, 1995 (taxonomy source)
Corallochytriidae Cavalier-Smith, 1995 (current name source)
Corallochytriidae Cavalier-Smith, 1995 (extant flag source)
Corallochytriidae Cavalier-Smith, 1995 (basis of record)
Corallochytrium Raghu-Kumar, 1987 (verified source for family)
Coronympha H. Kirby, 1929 (verified source for family)
Craspedida (additional source)
Creolimacidae Cavalier-Smith, 2013 (original description)
Creolimacidae Cavalier-Smith, 2013 (current name source)

 Taxonomic remark

 for Discocelia Cavalier-Smith, 2013

Nomen novum for Discocelis Vørs, 1988, non Discocelis Ehrenberg, 1836 (Platyhelminthes). [details]

 Taxonomic remark

 for Discocelida

Placed in Placoperla by Cavalier-Smith et al., 2018 and in Cercozoa (Placonuda) in Ruggiero et al., 2015; previously in ... [details]

 Taxonomic remark

 for Discocelis Vørs, 1988

Junior homonym of Discocelis Ehrenberg, 1836 (Platyhelminthes); replacement name is Discohelia Cavalier-Smith, 2013. [details]

 Taxonomic remark

 for Ichthyophonidae Cavalier-Smith, 2013

Originally as Ichthyophonaceae Rand, 1994, nomen nudum, refer Cavalier-Smith, 2013. [details]

 Taxonomic remark

 for Lamproderma Rostafinski, 1873

Family as given in Cavalier-Smith, 2013, although Lado & Eliasson, 2017 include this genus in Stemonitidaceae ... [details]

 Taxonomic remark

 for Lamprodermidae

Maintained as a distinct family by Cavalier-Smith, 2013 and Ruggiero, 2014, although Lado & Eliasson, 2017, include ... [details]

 Taxonomic remark

 for Pseudaphelidium Schweikert & Schnepf, 1996

Cavalier-Smith, 2013 does not include this genus in Aphelidiidae, considering it a neozoan incertae sedis. [details]

 Taxonomic remark

 for Psorospermium Hilgendorf, 1883

Junior homonym of Psorospermium Eimer, 1870 (Sporozoa); replacement name is Psorospermis Cavalier-Smith, 2013. [details]

 Taxonomic remark

 for Saccinobaculidae Cavalier-Smith, 2013

In use before 2013 but apparently not validly published, refer Cavalier-Smith, 2013. [details]