• Opephora P. Petit, 1888
• Opephora americana M.Peragallo, 1909 (uncertain > unassessed)
• Opephora angusta Cholnoky, 1956 (uncertain > unassessed)
• Opephora anomala Giffen, 1980 (uncertain > unassessed)
• Opephora ansata M.H.Hohn & J.Hellerman, 1963 (uncertain > unassessed)
• Opephora bituminosa (Pantocsek) Cleve-Euler, 1941 accepted as Fragilaria bituminosa var. bituminosa Pantocsek, 1889
• Opephora burchardtiae Witkowski (uncertain > unassessed)
• Opephora cantalense Héribaud-Joseph
• Opephora cantalense var. cantalense Héribaud, 1903 (uncertain > unassessed)
• Opephora cantalense var. capitata Héribaud, 1903 (uncertain > unassessed)
• Opephora cantalense var. obesa Héribaud, 1908 (uncertain > unassessed)
• Opephora cantalense var. obesa Tempère & Peragallo, 1912 (uncertain > unassessed)
• Opephora cantalense var. obtusa Tempère & Peragallo, 1912 (uncertain > unassessed)
• Opephora fragilarioides H. Kobayasi in Kobayasi et al., 1977 (uncertain > unassessed)
• Opephora gemmata (Grunow) Hustedt, 1931
• Opephora gemmata f. gemmata (Grunow) Hustedt, 1931 accepted as Sceptroneis gemmata Grunow, 1866 †
• Opephora gemmata f. minor Jurilj, 1957 (uncertain > unassessed)
• Opephora giffenii Schoeman in Schoeman & Meaton, 1982 (uncertain > unassessed)
• Opephora glangeaudi Héribaud, 1908 (uncertain > unassessed)
• Opephora guenter-grassii (Witkowski & Lange-Bertalot) Sabbe & Vyverman, 1995 accepted as Fragilaria guenter-grassii Witkowski & Lange-Bertalot, 1993 accepted as Staurosirella guenter-grassii (Witkowski & Lange-Bert.) E.Morales, C.E.Wetzel & Ector, 2019
• Opephora hachiroensis H. Kobayasi in Kobayasi et al., 1977 (uncertain > unassessed)
• Opephora horstiana Witkowski, 1994 (uncertain > unassessed)
• Opephora kittonii Cleve-Euler, 1941 (uncertain > unassessed)
• Opephora krumbeinii A.Witkowski, Witak & K.Stachura apud Lange-Bertalot & S.I.Genkal, 1999 accepted as Nanofrustulum krumbeinii (Witkowski, Witak & Stachura) E.Morales, 2019
• Opephora lanceolata K.E. Lohman, 1957 (uncertain > unassessed)
• Opephora linearis Sherm. & Partr., 1981 (uncertain > unassessed)
• Opephora lineata Edsbagge, 1968 (uncertain > unassessed)
• Opephora lineata Giffen, 1980 (uncertain > unassessed)
• Opephora marina (Gregory) Petit, 1888
• Opephora marina var. genuina Cleve-Euler, 1953 (uncertain > unassessed)
• Opephora marina var. marina (Gregory) Petit, 1888 accepted as Meridion marinum Gregory, 1857
• Opephora marina var. minuta Cleve-Euler, 1951 (uncertain > unassessed)
• Opephora marina var. perminuta (Grunow in Van Heurck) Proschkina-Lavrenko, 1950 accepted as Sceptroneis marina var. perminuta Grunow, 1881
• Opephora marina var. pontica Tarnavschi & Oltean, 1961 (uncertain > unassessed)
• Opephora martyi Héribaud-Joseph, 1902 accepted as Martyana martyi (Héribaud-Joseph) Round, 1990 accepted as Opephora martyi f. martyi Héribaud, 1902
• Opephora martyi f. anomala Héribaud, 1903 (uncertain > unassessed)
• Opephora martyi f. elliptica Komarenko in Komarenko & Vasilyeva, 1975 (uncertain > unassessed)
• Opephora martyi f. intermedia Komarenko in Komarenko & Vasilyeva, 1975 (uncertain > unassessed)
• Opephora martyi f. martyi Héribaud, 1902 (uncertain > unassessed)
• Opephora martyi f. semirostrata Tynni, 1994 (uncertain > unassessed)
• Opephora martyi f. vinaninkarenae Manguin, 1949 (uncertain > unassessed)
• Opephora martyi var. amphioxys Poretsky in Proschkina-Lavrenko, 1950 (uncertain > unassessed)
• Opephora martyi var. amphioxys Poretzky, 1953 (uncertain > unassessed)
• Opephora martyi var. baikalensis Skvortzow, 1937 (uncertain > unassessed)
• Opephora martyi var. capitata Héribaud-Joseph, 1903 (uncertain > unassessed)
• Opephora martyi var. elongata Skvortzow, 1936 (uncertain > unassessed)
• Opephora martyi var. minor Heribaud (uncertain > unassessed)
• Opephora martyi var. okadae (Skvortzow) Okuno, 1952 accepted as Opephora okadae Skvortzow, 1936
• Opephora martyi var. polymorpha (Jouravleva) Proschkina-Lavrenko, 1950 accepted as Opephora polymorpha Jouravleva, 1936
• Opephora martyi var. robusta Héribaud, 1903 (uncertain > unassessed)
• Opephora martyi var. robusta Skvortzow, 1936 (uncertain > unassessed)
• Opephora minuta (Cleve-Euler) A.Witkowski, H.Lange-Bertalot & D.Metzeltin, 2000 (uncertain > unassessed)
• Opephora mutabilis (Grunow) Sabbe & Vyverman, 1995 accepted as Sceptroneis mutabilis var. mutabilis Grunow in Cleve & Möller, 1879
• Opephora naveana R.Le Cohu, 1988 (uncertain > unassessed)
• Opephora neoelliptica (A.Witkowski) A.Witkowski, D.Metzeltin & Lange-Bertalot, 1996 (uncertain > unassessed)
• Opephora okadae Skvortzow, 1936 (uncertain > unassessed)
• Opephora olsenii Møller, 1950 (uncertain > unassessed)
• Opephora pacifica (Grunow) Petit, 1888
• Opephora pacifica f. pacifica (Grunow) Petit, 1888 accepted as Fragilaria pacifica var. pacifica Grunow, 1862
• Opephora pacifica f. parva Mereschkowsky, 1902 (uncertain > unassessed)
• Opephora pacifica var. trigona Heribaud (uncertain > unassessed)
• Opephora parva (Grunow) Krasske, 1939 accepted as Sceptroneis marina var. parva Grunow, 1881
• Opephora perlonga Giffen, 1967 (uncertain > unassessed)
• Opephora perlonga var. clavata Giffen, 1967 (uncertain > unassessed)
• Opephora perminuta (Grunow) Frenguelli, 1938 accepted as Sceptroneis marina var. perminuta Grunow, 1881
• Opephora pinnata Ehrenberg
• Opephora pinnata var. lanceolata Boyer, 1916 (uncertain > unassessed)
• Opephora pinnata var. pinnata Petit, 1888 (uncertain > unassessed)
• Opephora polymorpha Jouravleva, 1936 (uncertain > unassessed)
• Opephora schulzi (Brockmann) Simonsen, 1962 accepted as Fragilaria schulzii C.Brockmann, 1950
• Opephora schwartzii (Grunow) Petit ex Pelletan, 1889
• Opephora schwarzii (Grunow) Cleve-Euler, 1953 (uncertain > unassessed)
• Opephora schwarzii (Grunow) Petit ex Pelletan, 1889 accepted as Fragilaria schwartzii Grunow, 1863
• Opephora taiaensis Carter & Denny, 1982 (uncertain > unassessed)