• 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
• Alveocymba mirabilis (Hustedt) Kapustin, Kulikovskiy & Kociolek in Kapustin et al., 2020
• Anomoeoneis atacamensis Frenguelli, 1934
• Anomoeoneis bicapitata Andrews, 1971 (uncertain > unassessed)
• Anomoeoneis biceps (Ehrenberg) Fricke, 1902 accepted as Navicula biceps var. biceps Ehrenberg, 1843
• Anomoeoneis bipunctata (Grunow in Van Heurck) Cleve, 1895 accepted as Navicula bipunctata Grunow in Van Heurck, 1880
• Anomoeoneis bohemica (Ehrenberg) Pfitzer, 1871 accepted as Navicula bohemica f. bohemica Ehrenberg, 1854
• Anomoeoneis bohemica (Ehrenberg) Reinhard, 1913 accepted as Anomoeoneis costata (Kützing) Hustedt, 1959 accepted as Navicula costata var. costata Kützing, 1844
• Anomoeoneis bonnieri ‘Lauby' Mills, 1933 (uncertain > unassessed)
• Anomoeoneis brachysira (Brébisson ex Rabenhorst) Cleve, 1895 accepted as Brachysira brebissonii R.Ross, 1986 accepted as Brachysira brebissonii f. brebissonii R.Ross, 1986
• Anomoeoneis brachysira f. acutiuscula Cleve-Euler, 1934 (uncertain > unassessed)
• Anomoeoneis brachysira f. brachysira (Brébisson in Rabenhorst) Cleve, 1895 accepted as Navicula brachysira Brébisson ex Rabenhorst, 1853
• Anomoeoneis brachysira f. genuina Cleve-Euler, 1953 (uncertain > unassessed)
• Anomoeoneis brachysira f. inflata Mayer, 1933 (uncertain > unassessed)
• Anomoeoneis brachysira f. minima (Grunow in Van Heurck) Cleve-Euler, 1953 accepted as Navicula serians var. minima Grunow, 1880
• Anomoeoneis brachysira f. quadripunctata Cleve-Euler, 1953 (uncertain > unassessed)
• Anomoeoneis brachysira f. subacuminata (Mayer) Cleve-Euler, 1953 accepted as Anomoeoneis exilis f. subacuminata Mayer, 1919
• Anomoeoneis brachysira f. thermalis (Grunow) Woodhead & Tweed, 1953 accepted as Navicula serians var. thermalis Grunow, 1880
• Anomoeoneis brachysira var. elliptica Cleve-Euler, 1939 (uncertain > unassessed)
• Anomoeoneis brachysira var. lanceolata (Mayer) Cleve-Euler, 1953 accepted as Anomoeoneis exilis var. lanceolata Mayer, 1919
• Anomoeoneis brachysira var. oblonga Mayer, 1933 (uncertain > unassessed)
• Anomoeoneis brachysira var. thermalis (Grunow) Cleve-Euler, 1953 accepted as Navicula serians var. thermalis Grunow, 1880
• Anomoeoneis brachysira var. zellensis (Grunow) K.Krammer, 1986 accepted as Navicula zellensis var. zellensis Grunow, 1860
• Anomoeoneis canadensis Woodhead & Tweed, 1960 (uncertain > unassessed)
• Anomoeoneis chilensis Krasske, 1939 accepted as Nupela chilensis (Krasske) Lange-Bertalot in Lange-Bertalot & Moser, 1994
• Anomoeoneis concreta Frenguelli, 1936
• Anomoeoneis costata (Kützing) Hustedt, 1959 accepted as Navicula costata var. costata Kützing, 1844
• Anomoeoneis costata var. brachysira (Breb. Ex Rabenh) Hust. accepted as Anomoeoneis costata (Kützing) Hustedt, 1959 accepted as Navicula costata var. costata Kützing, 1844
• Anomoeoneis costata var. tibetica C.C.Jao (uncertain)
• Anomoeoneis cubita K.E. Lohman, 1957 (uncertain > unassessed)
• Anomoeoneis decipiens (uncertain > unassessed)
• Anomoeoneis decipiens var. decipiens Cleve-Euler, 1953 (uncertain > unassessed)
• Anomoeoneis decipiens var. densestriata Cleve-Euler, 1953 (uncertain > unassessed)
• Anomoeoneis decipiens var. hybrida Cleve-Euler, 1953 (uncertain > unassessed)
• Anomoeoneis decipiens var. typica Cleve-Euler, 1953 (uncertain > unassessed)
• Anomoeoneis diaphanae Manguin in Guermeur, 1954 (uncertain > unassessed)
• Anomoeoneis dickiei Jousé, 1939 (uncertain > unassessed)
• Anomoeoneis dumbeana Maillard, 1978 (uncertain > unassessed)
• Anomoeoneis elliptica Zakrzewski, 1934 (uncertain > unassessed)
• Anomoeoneis exellii Salah, 1953 (uncertain > unassessed)
• Anomoeoneis exilis (Kützing) Cleve, 1895 accepted as Navicula exilis Kützing, 1844
• Anomoeoneis exilis f. exilis (Kützing) Cleve, 1895 accepted as Navicula exilis f. exilis Kützing, 1844
• Anomoeoneis exilis f. gibbosa Foged, 1980 (uncertain > unassessed)
• Anomoeoneis exilis f. intermedia Kiselev-Vozzhennikova, 1950 (uncertain > unassessed)
• Anomoeoneis exilis f. lanceolata (A. Mayer) Hustedt, 1959 accepted as Anomoeoneis exilis var. lanceolata Mayer, 1919
• Anomoeoneis exilis f. subacuminata Mayer, 1919 (uncertain > unassessed)
• Anomoeoneis exilis f. undulata Kisselev, 1955 (uncertain > unassessed)
• Anomoeoneis exilis var. azorica Manguin, 1942 (uncertain > unassessed)
• Anomoeoneis exilis var. genuina Mayer, 1919 (uncertain > unassessed)
• Anomoeoneis exilis var. gomphonemacea (Grunow) Cleve, 1895 accepted as Navicula gomphonemacea Grunow in Van Heurck, 1880
• Anomoeoneis exilis var. lanceolata Mayer, 1919 (uncertain > unassessed)
• Anomoeoneis exilis var. minor Krasske, 1939 (uncertain > unassessed)
• Anomoeoneis exilis var. nipponica Skvortzow, 1936 (uncertain > unassessed)
• Anomoeoneis exilis var. speciosa Rampi, 1943 (uncertain > unassessed)
• Anomoeoneis exilis var. thermalis (Grunow) Cleve, 1895 accepted as Navicula serians var. thermalis Grunow, 1880
• Anomoeoneis fogedii Reimer, 1982 (uncertain > unassessed)
• Anomoeoneis follis (Ehrenberg) Cleve, 1895 † accepted as Brachysira follis (Ehrenberg) R.Ross, 1986 accepted as Navicula follis Ehrenberg, 1838 †
• Anomoeoneis follis var. follis (Ehrenberg) Cleve, 1895 accepted as Navicula follis Ehrenberg, 1838 †
• Anomoeoneis follis var. fossilis Reimer, 1961 † (uncertain > unassessed)
• Anomoeoneis follis var. hannae Reimer, 1961 † (uncertain > unassessed)
• Anomoeoneis formidolosa Cholnoky, 1959 (uncertain > unassessed)
• Anomoeoneis frenguellii Manguin in Bourrelly & Manguin, 1952 (uncertain > unassessed)
• Anomoeoneis garrensis Lange-Bertalot & Krammer, 1985 (uncertain > unassessed)
• Anomoeoneis gomphonemacea (Grunow) Kobayashi, 1969 accepted as Navicula gomphonemacea Grunow in Van Heurck, 1880
• Anomoeoneis gomphonemoides Maillard, 1978 (uncertain > unassessed)
• Anomoeoneis grandis Zakrzewski, 1934 (uncertain > unassessed)
• Anomoeoneis hungarica Hajós, 1959 (uncertain > unassessed)
• Anomoeoneis inconcinna D. Metzeltin, H. Lange-Bertalot & S. Nergui, 2009 (uncertain > unassessed)
• Anomoeoneis intermedia Østrup, 1910 (uncertain > unassessed)
• Anomoeoneis irawanae Podzorski & Håkansson, 1987 (uncertain > unassessed)
• Anomoeoneis kolbei Skvortzow, 1971 (uncertain > unassessed)
• Anomoeoneis lanceolata Gandhi, 1959
• Anomoeoneis lanceolata K.E. Lohman, 1957 (uncertain > unassessed)
• Anomoeoneis lignerii (Lauby) F.W. Mills, 1933 accepted as Navicula ligneri Lauby, 1910
• Anomoeoneis longirostris Hustedt, 1942 (uncertain > unassessed)
• Anomoeoneis macdonaghi (Frenguelli) Luchini & Verona, 1972
• Anomoeoneis macdonaghi Frenguelli, 1929 accepted as Anomoeoneis macdonaghi (Frenguelli) Luchini & Verona, 1972
• Anomoeoneis macdonaghi Frenguelli, 1929 (uncertain > unassessed)
• Anomoeoneis macraeana (Pantocsek) Cleve, 1895 accepted as Navicula macraeana Pantocsek, 1889
• Anomoeoneis malinvaudi (Héribaud) Amossé, 1921 accepted as Navicula malinvaudi Héribaud, 1902
• Anomoeoneis malinvaudi var. minor Amossé, 1921 (uncertain > unassessed)
• Anomoeoneis manginii Amossé
• Anomoeoneis manginii f. mangini Amossé, 1921 (uncertain > unassessed)
• Anomoeoneis manginii f. minor Amossé, 1921 (uncertain > unassessed)
• Anomoeoneis menilitica (Pantocsek) Cleve, 1895 accepted as Navicula menilitica Pantocsek, 1889
• Anomoeoneis microcephala A. Berg, 1945 (uncertain > unassessed)
• Anomoeoneis minor Krasske, 1939 (uncertain > unassessed)
• Anomoeoneis neocaledonica Maillard, 1978 (uncertain > unassessed)
• Anomoeoneis neocaledonica var. angusta Maillard, 1978 (uncertain > unassessed)
• Anomoeoneis nyensis K.E. Lohman, 1957 (uncertain > unassessed)
• Anomoeoneis okadae Skvortzov, 1938 (uncertain > unassessed)