Diploneis abscondita Lange–Bertalot & G. Hofmann, 2016
Diploneis aculeata Anisimova, 1951 (uncertain > unassessed )
Diploneis adeliae Manguin, 1960 (uncertain > unassessed )
Diploneis adiaphana Schrader, 1969 (uncertain > unassessed )
Diploneis adonis (J.Brun) Cleve, 1894 accepted as Navicula adonis var. adonis Brun in Brun & Tempère, 1889
Diploneis adonis subsp. oamaruensis Cleve, 1894 accepted as Diploneis oamaruensis (Cleve) Mills, 1934 accepted as Diploneis adonis var. oamaruensis Cleve, 1894
Diploneis adonis var. ganymedes Cleve, 1894 (uncertain > unassessed )
Diploneis adonis var. gibbosa (Brun in Brun & Tempère) Cleve, 1894 accepted as Navicula adonis var. gibbosa Brun in Brun & Tempère, 1889
Diploneis adonis var. oamaruensis Cleve, 1894 (uncertain > unassessed )
Diploneis adonis var. tiltilensis (Schmidt in Schmidt et al.) Cleve, 1894 accepted as Diploneis adonis var. tiltilensis Frenguelli, 1949
Diploneis adonis var. tiltilensis Frenguelli, 1949 (uncertain > unassessed )
Diploneis advena (A.Schmidt) Cleve, 1894
Diploneis advena var. advena (Schmidt in Schmidt et al.) Cleve, 1894
Diploneis advena var. japonica Meister, 1935 (1935) (uncertain > unassessed )
Diploneis advena var. parca (Schmidt in Schmidt et al.) Cleve, 1894 (uncertain > unassessed )
Diploneis advena var. recta (Brun & Heribaud in Heribaud) Cleve, 1894 accepted as Navicula recta Brun & Héribaud in Héribaud, 1893
Diploneis advena var. sansegana (Grunow) Cleve, 1894 accepted as Navicula sansegana Grunow, 1875
Diploneis advena var. schmidtti Heiden & Kolbe, 1928 (uncertain > unassessed )
Diploneis aequorea H.Heiden (uncertain > unassessed )
Diploneis aestica (uncertain > unassessed )
Diploneis aestica var. oamaruensis (Cleve) Desikachary & Sreelatha, 1989 accepted as Diploneis fusca var. oamaruensis Cleve, 1894
Diploneis aestiva (Donkin) Cleve, 1894 accepted as Diploneis aestiva var. aestiva (Donkin) Cleve, 1894
Diploneis aestiva f. alpha Cleve, 1894 (uncertain > unassessed )
Diploneis aestiva f. beta Cleve, 1894 (uncertain > unassessed )
Diploneis aestiva f. major (H. Peragallo & M. Peragallo) T.V. Desikachary, 1989 accepted as Navicula fusca var. major Peragallo & Peragallo, 1897
Diploneis aestiva var. aestiva (Donkin) Cleve, 1894
Diploneis aestiva var. delicata (A.Schmidt) R.Ross, 1986 accepted as Navicula fusca var. delicata A.Schmidt, 1874
Diploneis aestiva var. fusca (Gregory) R.Ross, 1986 accepted as Navicula smithii var. fusca Gregory, 1857
Diploneis aestiva var. rhombica (Petit) F.W. Mills, 1934 accepted as Navicula aestiva var. rhombica Petit, 1904
Diploneis aestuari Hustedt, 1939 (uncertain > unassessed )
Diploneis aestuarii Hustedt, 1939 accepted as Diploneis aestuari Hustedt, 1939
Diploneis aethiopum Ehrenberg, 1854 (uncertain > unassessed )
Diploneis africana H.Heiden (uncertain > unassessed )
Diploneis alpina Meister, 1912 (uncertain > unassessed )
Diploneis alpina f. baicalensis Skvortzow & Meyer, 1928 (uncertain > unassessed )
Diploneis alpina var. subconstricta (A.Cleve) Cleve-Euler (uncertain > unassessed )
Diploneis altana Kulikovskiy & Lange-Bertalot in Kulikovskiy et al., 2015
Diploneis amicula Kulikovskiy & Lange-Bertalot in Kulikovskiy et al., 2015
Diploneis amphisbaena Manicharova, 1950 (uncertain > unassessed )
Diploneis andama Kulikovskiy & Lange-Bertalot in Kulikovskiy et al., 2015
Diploneis andesitica (Pantocsek) F.W. Mills, 1934 accepted as Navicula andesitica Pantocsek, 1889
Diploneis andina Frenguelli, 1942 accepted as Muelleria andina (Frenguelli) Guerrero, Vouilloud & Serino 2024
Diploneis angusta Jovanovska et al., 2023
Diploneis antinitescens (M.Peragallo) F.W.Mills, 1934 accepted as Navicula antinitescens M.Peragallo, 1908
Diploneis antiqua Cleve-Euler, 1953 (uncertain > unassessed )
Diploneis aokiensis M.Idei, 2013
Diploneis apis (Donkin) F.W. Mills, 1934 (uncertain > unassessed )
Diploneis apis (Ehrenberg) Ehrenberg, 1845 accepted as Pinnularia apis Ehrenberg, 1843
Diploneis apis (Kützing) F.W. Mills, 1934 (uncertain > unassessed )
Diploneis arctica (Lange–Bertalot) Lange–Bertalot & A. Fuhrmann, 2016
Diploneis arctica Cleve, 1898 (uncertain > unassessed )
Diploneis areolata Cleve, 1894 (uncertain > unassessed )
Diploneis argentina (Frenguelli) Frenguelli, 1945
Diploneis atmosphaerica (Ehrenberg) R.Jahn & W.-H.Kusber, 2004 accepted as Cocconeis atmosphaerica Ehrenberg, 1854
Diploneis baicalensis Skvortzov & Meyer, 1928 (uncertain > unassessed )
Diploneis baicaloculata Kulikovskiy & Lange-Bertalot in Kulikovskiy et al., 2015
Diploneis baicaloparma Kulikovskiy & Lange-Bertalot in Kulikovskiy et al., 2015
Diploneis baicalpetersenii Kulikovskiy & Lange-Bertalot in Kulikovskiy et al., 2015
Diploneis balcanica N.G.Ognjanova-Rumenova & K.Buczkó, 2010
Diploneis barbatula Skvortzov, 2012 (uncertain )
Diploneis basilica (Brun) F.W. Mills, 1934 accepted as Navicula basilica Brun, 1891
Diploneis beyrichiana (A.Schmidt) A.Amossé, 1924 accepted as Navicula beyrichiana f. beyrichiana Schmidt in Schmidt et al., 1881
Diploneis beyrichiana f. minor (Pantocsek) Cleve, 1894 accepted as Navicula beyrichiana var. minor Pantocsek in Cleve, 1894
Diploneis beyrichiana var. lesinensis (Grunow) F.W. Mills, 1934 accepted as Diploneis lesinensis Cleve, 1894
Diploneis beyrichiana var. moravica Cleve, 1894 (uncertain > unassessed )
Diploneis binaria (Schmidt in Schmidt et al.) Cleve, 1894 accepted as Navicula binaria Schmidt in Schmidt et al., 1875
Diploneis bioculata (Grunow in Schmidt et al.) Cleve, 1894 accepted as Navicula bioculata var. bioculata Grunow in Schmidt et al., 1881
Diploneis bioculata var. vittata Cleve, 1894 (uncertain > unassessed )
Diploneis biremiformis S.J.M. Droop, 1998 (uncertain > unassessed )
Diploneis biseriata Cleve, 1894 (uncertain > unassessed )
Diploneis biseriata var. australis Desikachary & Prema in Desikachary, 1988 (uncertain > unassessed )
Diploneis biseriata var. galapagensis Cleve, 1894 (uncertain > unassessed )
Diploneis biseriata var. lata Cleve, 1894 (uncertain > unassessed )
Diploneis boldtiana Cleve, 1891 (uncertain > unassessed )
Diploneis boldtiana var. acuminata Playfair, 1914 (uncertain > unassessed )
Diploneis boldtiana var. australica Playfair, 1914 (uncertain > unassessed )
Diploneis boldtiana var. baikalensis Skvortzow, 1937 (uncertain > unassessed )
Diploneis boldtiana var. ovalis Playfair, 1914 (uncertain > unassessed )
Diploneis boldtiana var. punctata Cleve-Euler, 1934 (uncertain > unassessed )
Diploneis boldtiana var. robusta Cleve-Euler, 1915 (uncertain > unassessed )
Diploneis bombiformis Cleve, 1894 (uncertain > unassessed )
Diploneis bomboides (A.W.F.Schmidt) Cleve, 1894 accepted as Navicula bomboides var. bomboides Schmidt, 1872
Diploneis bomboides f. minor Cleve, 1894
Diploneis bomboides var. intermedia F.W. Mills, 1934 (uncertain > unassessed )
Diploneis bomboides var. limanense (Heribaud & Peragallo in Heribaud) F.W. Mills, 1934 accepted as Navicula bomboides var. limanense Héribaud-Joseph
Diploneis bomboides var. madagascarensis Cleve, 1894 (uncertain > unassessed )
Diploneis bomboides var. madagascarensis f. minor Cleve accepted as Diploneis bomboides f. minor Cleve, 1894
Diploneis bomboides var. media (Grunow) Hustedt, 1937 accepted as Navicula bomboides var. media Grunow in Cleve & Grunow, 1880
Diploneis bomboides var. minor (Brun & Heribaud in Heribaud) F.W. Mills, 1934 accepted as Navicula bomboides var. minor Héribaud & Brun in Héribaud, 1902
Diploneis bomboides var. moesta (Schmidt in Schmidt et al.) Cleve, 1894 accepted as Navicula moesta Schmidt in Schmidt et al., 1881
Diploneis bombus (Ehrenberg) Ehrenberg, 1853 (uncertain > unassessed )
Diploneis bombus Cleve-Euler in Backman & Cleve-Euler Backman, 1922 accepted as Diploneis bombus (Ehrenberg) Ehrenberg, 1853
Diploneis bombus f. minor Cleve, 1899 (uncertain > unassessed )
Diploneis bombus var. bombiformis (Cleve) Hustedt, 1937 accepted as Diploneis bombiformis Cleve, 1894
Diploneis bombus var. bullata Cleve, 1890 (uncertain > unassessed )
Diploneis bombus var. densestriata (A.Schmidt) Cleve, 1894 accepted as Navicula gemina var. densestriata A.W.F.Schmidt, 1875
Diploneis bombus var. egena (A.Schmidt) Cleve, 1894 accepted as Navicula gemina var. egena A.Schmidt, 1875
Diploneis bombus var. egnea (A. Schmidt) Cleve, 1894
Diploneis bombus var. genuina Cleve-Euler, 1953 (uncertain > unassessed )
Diploneis bombus var. kuetzingi (Grunow) Hustedt, 1937 accepted as Navicula kuetzingii Grunow, 1860