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 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 accepted as Brachysira minor (Krasske) H. Lange-Bertalot, 1994
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 )
Anomoeoneis paludigena Scherer, 1988 accepted as Nupela paludigena (Scherer) Lange-Bertalot, 1993
Anomoeoneis palustris Maillard, 1978 (uncertain > unassessed )
Anomoeoneis pannonica (Grunow) Cholnoky, 1927 accepted as Navicula pannonica Grunow, 1860
Anomoeoneis polygramma (Ehrenberg) Cleve, 1895 accepted as Anomoeoneis costata (Kützing) Hustedt, 1959 accepted as Navicula costata var. costata Kützing, 1844
Anomoeoneis polygramma var. pannonica (Grunow) Frenguelli, 1934 accepted as Navicula pannonica Grunow, 1860
Anomoeoneis polygramma var. platensis Frenguelli, 1945 accepted as Anomoeoneis costata (Kützing) Hustedt, 1959 accepted as Navicula costata var. costata Kützing, 1844
Anomoeoneis polygramma var. polygramma (Ehrenberg) Cleve, 1895 accepted as Stauroneis polygramma Ehrenberg, 1843
Anomoeoneis polygramma var. rhomboides Jao, 1964 (uncertain > unassessed )
Anomoeoneis polygramma var. tibetica Jao, 1964 (uncertain > unassessed )
Anomoeoneis punae Maidana & Seeligman, 2015
Anomoeoneis rhetica Wuthrich, 1975 accepted as Nupela rhetica (Wuthrich) Lange-Bertalot, 1993
Anomoeoneis rhomboidea Krishnamurthy (uncertain > unassessed )