• Aphanothece Nägeli, 1849
• Aphanothece atrocrustacea Skuja, 1964
• Aphanothece baccilloidea Gardner, 1927
• Aphanothece bachmannii J. Komárková-Legnerová & G. Cronberg, 1994
• Aphanothece bacilloidea Gardner, 1927
• Aphanothece bacteriosa Komárek & Komárková-Legnerová, 2007 accepted as Anathece bacteriosa (Komárek & Komárková-Legnrová) Komárek, Kastovsky & Jezberová, 2011
• Aphanothece biceps Skuja, 1964
• Aphanothece botryosa Obuchova, 1965
• Aphanothece bullosa (Meneghini) Rabenhorst, 1865
• Aphanothece caerulescens (Borzì) Geitler, 1932 accepted as Bacularia caerulescens Borzì, 1905
• Aphanothece caldariorum Richter, 1880
• Aphanothece castagnei (Brébisson) Rabenhorst, 1865
• Aphanothece clathrata W. West & G.S. West, 1906
• Aphanothece clathratiformis Szafer, 1911 accepted as Chlorobium clathratiforme (Szafer, 1911) Imhoff, 2003
• Aphanothece cohenii Campbell & Golubic, 1985
• Aphanothece comasii J. Komárková-Legnerová & R. Tavera, 1996
• Aphanothece concerta Richter, Hauck & Richter
• Aphanothece conferta Richter, 1892
• Aphanothece conglomerata Rich, 1932
• Aphanothece cretaria Frémy, 1942
• Aphanothece curvata Lagerheim, 1883
• Aphanothece cylindracea (Gardner) Komárek & Anagnostidis, 1995
• Aphanothece desikacharyi F. Hindák, 1996
• Aphanothece elabens (Brébisson) Elenkin, 1938
• Aphanothece ellipsoidea (Schröder) Bourrelly, 1970 accepted as Rhabdogloea ellipsoidea Schröder, 1917
• Aphanothece endophytica (W. West & G.S. West) J. Komárková-Legnerová & G. Cronberg, 1994
• Aphanothece floccosa (Zalessky) G. Cronberg & J. Komárek, 1994
• Aphanothece gardneri de Toni, 1936
• Aphanothece gelatinosa (Hennings) Lemmermann, 1907
• Aphanothece gelatinosa Gardner, 1927 accepted as Aphanothece gardneri de Toni, 1936
• Aphanothece glebulenta Zalessky, 1926 accepted as Epigloeosphaera glebulenta (Zalessky) J. Komárková-Legnerová, 1991
• Aphanothece globosa Elenkin, 1938 accepted as Chroococcus globosus (Elenkin) Hindák, 1978
• Aphanothece goetzei Schmidle, 1901
• Aphanothece gracilis Schiller, 1954 accepted as Aphanothece clathrata W. West & G.S. West, 1906
• Aphanothece granulosa Nash, 1938
• Aphanothece halophytica Frémy, 1933
• Aphanothece hegewaldii Kovácik, 1988
• Aphanothece heterospora Rabenhorst, 1864
• Aphanothece karukerae Lami, 1938
• Aphanothece krumbeinii Campbell & Golubic, 1985
• Aphanothece le-jolisii Thuret, 1905 accepted as Aphanocapsa le-jolisii (Thuret) Frémy, 1924
• Aphanothece lemnae Chu, 1952
• Aphanothece longior Naumann, 1921
• Aphanothece luteola Schmidle, 1901 accepted as Chlorobium luteolum (Schmidle, 1901) Imhoff, 2003
• Aphanothece margaritacea (Kützing) Forti, 1907
• Aphanothece marina (Ercegovic) Komárek & Anagnostidis, 1995
• Aphanothece membranacea Rabenhorst, 1865 accepted as Gloeothece membranacea (Rabenhorst) Bornet, 1892
• Aphanothece microscopica Nägeli, 1849
• Aphanothece microspora (Meneghini) Rabenhorst, 1863 accepted as Aphanothece caldariorum Richter, 1880
• Aphanothece minor Frémy, 1941
• Aphanothece minutissima (W. West) J. Komárková-Legnerová & G. Cronberg, 1994
• Aphanothece mooreana (Harvey) Lagerheim, 1883 accepted as Aphanothece stagnina (Sprengel) A. Braun, 1863
• Aphanothece muralis (Tomaschek) Lemmermann, 1907 accepted as Aphanothece caldariorum Richter, 1880
• Aphanothece naegelii Wartmann, 1861
• Aphanothece nebulosa Skuja, 1964
• Aphanothece nidulans Richter, 1884
• Aphanothece nostocopsis Skuja, 1934
• Aphanothece opalescens Gardner, 1927
• Aphanothece packardii (Farlow) Setchell, 1917 accepted as Aphanothece utahensis Tilden, 1898
• Aphanothece pallida (Kützing) Rabenhorst, 1863
• Aphanothece paralleliformis G. Cronberg, 2003
• Aphanothece parallelliformis Cronberg, 2004
• Aphanothece piscinalis Rabenhorst, 1865 accepted as Aphanothece stagnina (Sprengel) A. Braun, 1863
• Aphanothece prasina A. Braun, 1863 accepted as Aphanothece stagnina (Sprengel) A. Braun, 1863
• Aphanothece protohydrae Häyrén, 1923
• Aphanothece pseudoglebulenta Joosten, 2006
• Aphanothece pulverulenta Bachmann, 1921 accepted as Aphanothece minutissima (W. West) J. Komárková-Legnerová & G. Cronberg, 1994
• Aphanothece rubra Liebetanz, 1925
• Aphanothece rufescens Hansgrig, 1892
• Aphanothece sacrum (Suringar) Okada, 1953
• Aphanothece salina Elenkin & Danilov, 1915
• Aphanothece saxicola Nägeli, 1849
• Aphanothece shiloi Campbell & Golubic, 1985 accepted as Cyanothece shiloi (Campbell & Golubic) Komárek & Anagnostidis, 1995
• Aphanothece smithii J. Komárková-Legnerová & G. Cronberg, 1994
• Aphanothece stagnina (Sprengel) A. Braun, 1863
• Aphanothece stratus Komárek & Cronberg, 2001
• Aphanothece subachroa Hansgirg, 1892 accepted as Aphanothece saxicola Nägeli, 1849
• Aphanothece thermalis Copeland, 1936
• Aphanothece thermicola Hindák, 1978
• Aphanothece trentepohlii (Mhor) Grunow, 1865 accepted as Aphanothece caldariorum Richter, 1880
• Aphanothece tuberculata (Areschoug) Forti, 1907 accepted as Aphanothece stagnina (Sprengel) A. Braun, 1863
• Aphanothece uliginosa Taylor, 1928
• Aphanothece utahensis Tilden, 1898
• Aphanothece variabilis (Schiller) Komárek, 1995
• Aphanothece viennensis Schiller, 1954 accepted as Rhabdoderma lineare Schmidle & Lauterborn, 1900
• Aphanothece zulanirae Werner & Sant'Anna