• Trachyneis P.T. Cleve, 1894
• Trachyneis antarctica Heiden & Kolbe, 1928 (uncertain > unassessed)
• Trachyneis antillarum (Cleve & Grunow) Cleve
• Trachyneis antillarum var. antillarum (Cleve & Grunow in Cleve) Cleve, 1894 accepted as Alloioneis antillarum Cleve & Grunow in Cleve, 1878
• Trachyneis antillarum var. kurzii (Grunow in Cleve) Cleve, 1894 accepted as Navicula kurzii Grunow in Cleve, 1878
• Trachyneis aspera (Ehrenberg) Cleve, 1894
• Trachyneis aspera f. intermedia (Grunow in Schmidt et al.) Cleve, 1894 accepted as Navicula aspera var. interolmedia Grunow in Schmidt et al., 1876
• Trachyneis aspera f. robusta Østrup, 1910 (uncertain > unassessed)
• Trachyneis aspera var. amphora (Brun) Cleve, 1894 accepted as Navicula amphora Brun, 1891
• Trachyneis aspera var. angusta (W.Smith) Cleve, 1894 (uncertain > unassessed)
• Trachyneis aspera var. antarctica M. Peragallo, 1921 (uncertain > unassessed)
• Trachyneis aspera var. aspera (Ehrenberg; Ehrenberg) Cleve, 1894 accepted as Navicula aspera Ehrenberg, 1840
• Trachyneis aspera var. asymmetrica Qi, Lin & Zhang in Qi, Lin, Zhang & He, 1986 (uncertain > unassessed)
• Trachyneis aspera var. atomus Hagelstein, 1939 (uncertain > unassessed)
• Trachyneis aspera var. californica Cleve, 1894 (uncertain > unassessed)
• Trachyneis aspera var. chinensis Skvortzow, 1932 (uncertain > unassessed)
• Trachyneis aspera var. contermina (Schmidt) Cleve, 1894 accepted as Navicula contermina Schmidt in Schmidt et al., 1876
• Trachyneis aspera var. debyi Grove Collection (uncertain > unassessed)
• Trachyneis aspera var. derasa Cleve, 1894 (uncertain > unassessed)
• Trachyneis aspera var. elliptica Hendey, 1964 (uncertain > unassessed)
• Trachyneis aspera var. genuina Cleve, 1894 (uncertain > unassessed)
• Trachyneis aspera var. gianfranceschii Zanon, 1929 (uncertain > unassessed)
• Trachyneis aspera var. javanicus (Hustedt in Schmidt et al.) F.W. Mills, 1935 accepted as Trachyneis javanicus (Hustedt in Schmidt et al.)
• Trachyneis aspera var. magnipunctata Manguin, 1960 (uncertain > unassessed)
• Trachyneis aspera var. minuta H. Peragallo & M. Peragallo, 1898 (uncertain > unassessed)
• Trachyneis aspera var. neumeyeri (Janisch in Schmidt et al.) Cleve, 1894 accepted as Navicula neumayeri Janisch in Schmidt et al., 1876
• Trachyneis aspera var. oblonga (J.W.Bailey) Cleve, 1894 accepted as Stauroptera oblonga J.W. Bailey, 1854
• Trachyneis aspera var. orientalis Skvortzov, 1929 (uncertain > unassessed)
• Trachyneis aspera var. parallela Woodhead & Tweed, 1960 (uncertain > unassessed)
• Trachyneis aspera var. perobliqua Cleve, 1894 (uncertain > unassessed)
• Trachyneis aspera var. producta Chin & Cheng, 1979 (uncertain > unassessed)
• Trachyneis aspera var. pulchella (W.Smith) Cleve, 1894 accepted as Stauroneis pulchella W.Smith, 1853
• Trachyneis aspera var. pulchella sensu Peragallo & Peragallo, 1897-1908 (uncertain > unassessed)
• Trachyneis aspera var. residua (A.Schmidt) Cleve, 1894 accepted as Navicula residua Schmidt in Schmidt et al., 1876
• Trachyneis aspera var. rhombica Cleve, 1894 (uncertain > unassessed)
• Trachyneis aspera var. robusta (Petit) Cleve, 1894 accepted as Stauroneis robusta Petit, 1877
• Trachyneis aspera var. sabangi Meister, 1932 (uncertain > unassessed)
• Trachyneis aspera var. schmidtiana (Grunow in Schmidt et al.) Cleve, 1894 accepted as Navicula schmidtiana Grunow in Schmidt et al., 1876
• Trachyneis aspera var. unilatera Chin & Cheng, 1979 (uncertain > unassessed)
• Trachyneis aspera var. vulgaris Cleve, 1894 (uncertain > unassessed)
• Trachyneis australis (Petit) Woodhead & Tweed, 1958 (uncertain > unassessed)
• Trachyneis barbadensis Boyer, 1922 (uncertain > unassessed)
• Trachyneis brunii (Cleve ex Brun) Cleve, 1894 (uncertain > unassessed)
• Trachyneis clepsydra (Donkin) Cleve, 1894
• Trachyneis clepsydra var. capinsis Petit, 1903 (uncertain > unassessed)
• Trachyneis clepsydra var. clepsydra (Donkin) Cleve, 1894 accepted as Navicula clepsydra var. clepsydra Donkin, 1861
• Trachyneis clepsydra var. scotia (Schmidt in Schmidt et al.) Cleve, 1894 accepted as Navicula scotica A.Schmidt, 1876
• Trachyneis debyi (Leuduger-Fortmorel) Cleve, 1894 accepted as Alloioneis debyi Leuduger-Fortmorel, 1892
• Trachyneis formosa Meister, 1932 (uncertain > unassessed)
• Trachyneis hungarica (Pantocsek) Frenguelli, 1949 accepted as Navicula aspera var. hungarica Pantocsek, 1889
• Trachyneis intermedium (Grunow) Bailey, 1924 accepted as Navicula aspera var. interolmedia Grunow in Schmidt et al., 1876
• Trachyneis javanicus (Hustedt in Schmidt et al.) (uncertain > unassessed)
• Trachyneis johnsoniana (Greville) Cleve, 1894 accepted as Navicula johnsoniana Greville, 1863
• Trachyneis minor Chin & Cheng, 1979 (uncertain > unassessed)
• Trachyneis oblonga J.W.Bailey accepted as Trachyneis aspera var. oblonga (J.W.Bailey) Cleve, 1894 accepted as Stauroptera oblonga J.W. Bailey, 1854
• Trachyneis oblonga var. minor M. Peragallo, 1924 (uncertain > unassessed)
• Trachyneis oblonga var. oblonga (J.W. Bailey) H. Peragallo & M. Peragallo, 1898 accepted as Stauroptera oblonga J.W. Bailey, 1854
• Trachyneis olivaeformis Chin & Cheng, 1979 (uncertain > unassessed)
• Trachyneis pulchella (Small) Bailey, 1924 (uncertain > unassessed)
• Trachyneis robusta (Petit) H. Peragallo & M. Peragallo, 1898 accepted as Stauroneis robusta Petit, 1877
• Trachyneis rostratus (Hustedt in Schmidt et al.) (uncertain > unassessed)
• Trachyneis schmidtiana (Grunow in Schmidt et al.) H. Peragallo & M. Peragallo, 1898 accepted as Navicula schmidtiana Grunow in Schmidt et al., 1876
• Trachyneis schmidtii (uncertain > unassessed)
• Trachyneis schmidtii var. africana Heiden & Kolbe, 1928 (uncertain > unassessed)
• Trachyneis schmidtii var. schmidtii Heiden & Kolbe, 1928 (uncertain > unassessed)
• Trachyneis sieboldii (Pantocsek) Tsumura, 1967 accepted as Navicula sieboldii Pantocsek, 1892
• Trachyneis speibonae Giffen, 1970 (uncertain > unassessed)
• Trachyneis sumatrensis (Leuduger-Fortmorel) F.W. Mills, 1935 accepted as Navicula sumatrensis Leuduger-Fortmorel, 1892
• Trachyneis tumidula (Grunow) Cleve, 1894 accepted as Stauroneis tumidula Grunow, 1860
• Trachyneis velata A.Schmidt
• Trachyneis velata f. alternata Giffen, 1980 (uncertain > unassessed)
• Trachyneis velata var. notata Mereschkowsky, 1902 (uncertain > unassessed)
• Trachyneis velata var. oblonga Chin & Cheng, 1979 (uncertain > unassessed)
• Trachyneis velata var. ornata Meister, 1937 (uncertain > unassessed)
• Trachyneis velata var. rhomboidea M. Peragallo in Tempère & Peragallo, 1908 (uncertain > unassessed)
• Trachyneis velata var. velata (Schmidt in Schmidt et al.) Cleve, 1894 accepted as Navicula velata Schmidt in Schmidt et al., 1876
• Trachyneis velatoides Ricard, 1975 (uncertain > unassessed)
• Trachyneis vulgaris (Cleve) Bailey, 1924 (uncertain > unassessed)