Afrocymbella aschersonii (Otto Müller) K.Krammer, 2003 accepted as Gomphocymbella aschersonii var. aschersonii Otto Müller, 1905
Afrocymbella beccarii (Grunow) K.Krammer, 2003 accepted as Caloneis vandermerwei Cholnoky, 1957
Afrocymbella gracilis (Hustedt) Krammer, 2003 accepted as Gomphocymbella gracilis Hustedt, 1931
Afrocymbella kociolekii K.Krammer, 2003 (uncertain > unassessed )
Afrocymbella muelleri (Kociolek & Stoermer) K.Krammer, 2003 accepted as Gomphocymbella muelleri Kociolek & Stoermer, 1993
Afrocymbella muelleri var. acuminata K.Krammer, 2003 (uncertain > unassessed )
Afrocymbella pergracilis K.Krammer, 2003 (uncertain > unassessed )
Afrocymbella reichardtii K.Krammer, 2003 (uncertain > unassessed )
Afrocymbella reichardtii var. procera K.Krammer, 2003 (uncertain > unassessed )
Afrocymbella tanganikae (Kociolek & Stoermer) K. Krammer, 2003 accepted as Gomphocymbella tanganyikae Kociolek & Stoermer, 1993
Gomphocymbella ancyli (Cleve) Hustedt, 1930 † accepted as Cymbella ancyli Cleve, 1902 †
Gomphocymbella aschersonii Otto Müller, 1905 accepted as Afrocymbella aschersonii (Otto Müller) K.Krammer, 2003 accepted as Gomphocymbella aschersonii var. aschersonii Otto Müller, 1905
Gomphocymbella aschersonii var. aschersonii Otto Müller, 1905 (uncertain > unassessed )
Gomphocymbella aschersonii var. rigida Zanon, 1941 (uncertain > unassessed )
Gomphocymbella asymmetrica Shi & Li, 2003 †
Gomphocymbella beccarii (Grunow) Forti, 1910 accepted as Cymbella beccarii Grunow, 1886
Gomphocymbella brunellii Zanon, 1941 (uncertain > unassessed )
Gomphocymbella bruni (Fricke) Otto Müller, 1905 accepted as Gomphonema bruni Fricke, 1902
Gomphocymbella canadensis Woodhead & Tweed, 1960 (uncertain > unassessed )
Gomphocymbella caudata Hajós, 1973 (uncertain > unassessed )
Gomphocymbella cymbella (Brun) Otto Müller, 1905 accepted as Gomphonema cymbella Brun, 1891
Gomphocymbella gracilis Hustedt, 1931 (uncertain > unassessed )
Gomphocymbella hungarica Hajós, 1968 (uncertain > unassessed )
Gomphocymbella incerta Iwahaschi, 1936 (uncertain > unassessed )
Gomphocymbella laxistria Shi & Li, 2003
Gomphocymbella miocenica Jousé, 1952 (uncertain > unassessed )
Gomphocymbella muelleri Kociolek & Stoermer, 1993 (uncertain > unassessed )
Gomphocymbella obliqua (Grunow) Otto Müller, 1905 accepted as Gomphonema commutatum var. obliqua Grunow, 1884
Gomphocymbella rossii J.P.Kociolek & E.F.Stoermer, 1993 (uncertain > unassessed )
Gomphocymbella ruttneri Hustedt, 1913 † (uncertain > unassessed )
Gomphocymbella sierraleonensis Woodhead & Tweed, 1960 (uncertain > unassessed )
Gomphocymbella sigmoidea Woodhead & Tweed, 1960 (uncertain > unassessed )
Gomphocymbella stadleriana Mayer, 1933 (uncertain > unassessed )
Gomphocymbella tanganyikae Kociolek & Stoermer, 1993 (uncertain > unassessed )
Gomphocymbella variabilis Jousé, 1952 (uncertain > unassessed )
Gomphocymbella vatovae Zanon, 1941 (uncertain > unassessed )
Gomphocymbella vulgaris (Kützing) Otto Müller, 1905 accepted as Sphenella vulgaris Kützing, 1844
Gomphoneis baicalensis (uncertain > unassessed )
Gomphoneis baicalensis var. baicalensis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis baicalensis var. elongata Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis baicaliana J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis basiorobusta You & Kociolek, 2013
Gomphoneis calcareum Cleve, 1868 (uncertain > unassessed )
Gomphoneis calcifuga (Lange-Bertalot & E.Reichardt) A.Tuji, 2005
Gomphoneis cantalica (Brun & Héribaud in Héribaud) Schmidt in Schmidt et al., 1899 accepted as Gomphonema cantalicum f. cantalicum Brun & Héribaud in Héribaud, 1893
Gomphoneis capitata J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis clevei (Fricke) Gil, 1989 accepted as Gomphonema clevei Fricke, 1902
Gomphoneis curta (Hustedt) Lange-Bertalot, 1978 accepted as Gomphonema curtum Hustedt, 1945
Gomphoneis distorta You & Kociolek, 2013
Gomphoneis elegans (Grunow) Cleve, 1894 †
Gomphoneis elegans var. baicalensis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis elegans var. elegans (Grunow in Van Heurck) Cleve, 1894 accepted as Gomphonema elegans var. elegans Grunow in Van Heurck, 1880
Gomphoneis elegans var. quadripunctata Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis eriense (Grunow) Skvortzow in Skvortzow & C.I.Meyer, 1928
Gomphoneis eriense f. baicalensis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis eriense f. hastata Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis eriense f. rostrata (M. Schmidt in Schmidt et al.) Skvortzow & Meyer, 1928 accepted as Gomphonema eriense var. rostrata M.Schmidt, 1899
Gomphoneis eriense var. angularis Kociolek & Stoermer, 1988
Gomphoneis eriense var. apiculata Stoermer in Reimer, 1982 (uncertain > unassessed )
Gomphoneis eriense var. apiculata Stoermer, 1963 (uncertain > unassessed )
Gomphoneis eriense var. baicalensis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis eriense var. canadensis Kociolek & Stoermer, 1988
Gomphoneis eriense var. eriense (Grunow) Skvortzow & Meyer, 1928 accepted as Gomphonema eriense var. eriense Grunow, 1878
Gomphoneis eriense var. rostrata (M.Schmidt) Skvortzow & Meyer, 1928 accepted as Gomphonema eriense var. rostrata M.Schmidt, 1899
Gomphoneis eriense var. variabilis Kociolek & Stoermer, 1988
Gomphoneis eriensioides M.S.Kulikovskiy, J.P.Kociolek & C.N.Solak, 2013
Gomphoneis eriensis (Grunow) Skvortzov & Meyer, 1928
Gomphoneis exigua (Kützing) Medlin
Gomphoneis fonticola (Hustedt) J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis fourtanierae J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis frenguellii Kociolek & Sala in Kociolek, Uyua, Sala, Santinelli & Cefarelli, 2017
Gomphoneis geitleri Kociolek & Stoermer, 1991 accepted as Gomphosinica geitleri (Kociolek & Stoermer) Kociolek, You & X.Wang, 2015
Gomphoneis gracile Bahls, 2017 accepted as Gomphoneis montana Bahls, 2017
Gomphoneis gracilis J.P.Kociolek, M.S.Kulikovskiy & C.N.Solak, 2013
Gomphoneis grandicapitata (Skabitchevsky) J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis hastata (Wislouch) Kociolek & Stoermer, 1988
Gomphoneis hastatoides J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis herculana accepted as Gomphoneis herculeana (Ehrenberg) Cleve, 1894
Gomphoneis herculeana (Ehrenberg) Cleve, 1894
Gomphoneis herculeana f. baicalensis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis herculeana var. abundans Kociolek & Stoermer, 1988
Gomphoneis herculeana var. clavata Cleve, 1894 †
Gomphoneis herculeana var. loweii Kociolek & Stoermer, 1988
Gomphoneis herculeana var. minuta Stone in McLaughlin & Stone, 1986 accepted as Gomphoneis minuta (Stone) Kociolek & Stoermer, 1988
Gomphoneis herculeana var. robusta (Grunow) Cleve, 1894
Gomphoneis herculeana var. rostrata Tempère & Peragallo, 1909 † accepted as Gomphoneis rostrata (Tempère & Peragallo) Kociolek & Stoermer, 1988
Gomphoneis herculeana var. septiceps M.Schmidt, 1899
Gomphoneis herculeanum accepted as Gomphoneis herculeana (Ehrenberg) Cleve, 1894
Gomphoneis herculeanum f. gracilis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Gomphoneis herculeanum var. clavata Cleve, 1894 (uncertain > unassessed )
Gomphoneis herculeanum var. herculeanum (Ehrenberg) Cleve, 1894 accepted as Gomphonema herculeanum var. herculeanum Ehrenberg, 1845
Gomphoneis herculeanum var. robusta (Grunow) Cleve, 1894 accepted as Gomphonema herculeanum var. robustum Grunow, 1878
Gomphoneis heterominuta Mayama & Kawashima, 2002 (uncertain > unassessed )
Gomphoneis impressa M.S.Kulikovskiy, J.P.Kociolek & C.N.Solak, 2013
Gomphoneis inconspicua J.P.Kociolek, M.S.Kulikovskiy & C.N.Solak, 2013
Gomphoneis lange-bertalotii J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis lata (Skabichevskij) J.P.Kociolek & M.S.Kulikovskiy, 2013
Gomphoneis linearis Kociolek & Stoermer, 1986
Gomphoneis magna Kociolek & Stoermer, 1990 †
Gomphoneis mamilla (Ehrenberg) Cleve, 1894 accepted as Gomphoneis mammilla (Ehremberg) Cleve, 1894