• Thalassionema A. Grunow ex C. Mereschkowsky, 1902
• Thalassionema antiqua Schrader, 1973 (uncertain > unassessed)
• Thalassionema bacillare (Heiden) Kolbe, 1955
• Thalassionema bacillaris (Heiden & Kolbe) Kolbe, 1955 accepted as Spinigera bacillaris Heiden, 1928
• Thalassionema bifurcum Kato & Suto, 2019 †
• Thalassionema capitulata (Castracane) Hustedt, 1958 accepted as Synedra capitulata Castracane, 1886
• Thalassionema claviformis Schrader, 1973 (uncertain > unassessed)
• Thalassionema curvatum Kisselev, 1935 (uncertain > unassessed)
• Thalassionema elegans Hustedt, 1958 (uncertain > unassessed)
• Thalassionema frauenfeldii (Grunow) Tempère & Peragallo, 1910
• Thalassionema frauenfeldii var. doljensis Tempère & Peragallo, 1910 (uncertain > unassessed)
• Thalassionema frauenfeldii var. frauenfeldii (Grunow) Tempère & Peragallo, 1910 accepted as Thalassiothrix frauenfeldii Cleve, 1894 accepted as Thalassionema frauenfeldii (Grunow) Tempère & Peragallo, 1910
• Thalassionema gelida (uncertain > unassessed)
• Thalassionema gelida var. elongata M. Peragallo, 1921 (uncertain > unassessed)
• Thalassionema gelida var. gelida M. Peragallo, 1921 (uncertain > unassessed)
• Thalassionema hirosakiensis (Kanaya) Schrader, 1973 accepted as Fragilaria hirosakiensis Kanaya, 1959
• Thalassionema javanicum (Grunow) Hasle in Hasle & Syvertsen, 1996 accepted as Thalassiothrix frauenfeldii var. javanica Grunow, 1881
• Thalassionema kuroshioensis Sugie & Ko.Suzuki, 2015
• Thalassionema lineatum Jousé, 1971 (uncertain > unassessed)
• Thalassionema nitzschioides (Grunow) Mereschkowsky, 1902
• Thalassionema nitzschioides f. curta (uncertain > unassessed)
• Thalassionema nitzschioides f. nitzschioides (Grunow) Van Heurck, 1896 accepted as Synedra nitzschioides f. nitzschioides Grunow, 1862 represented as Thalassionema nitzschioides (Grunow) Mereschkowsky, 1902
• Thalassionema nitzschioides var. acuminata (Grunow in Pantocsek) M. Peragallo, 1903 accepted as Synedra nitzschioides var. acuminata Grunow ex Pantocsek, 1886
• Thalassionema nitzschioides var. antiqua (Schrader) Moreno-Ruiz in Moreno-Ruiz & Licea, 1995 accepted as Thalassionema antiqua Schrader, 1973
• Thalassionema nitzschioides var. australis Cleve-Euler, 1949 (uncertain > unassessed)
• Thalassionema nitzschioides var. capitulata (Castracane) Moreno-Ruiz in Moreno-Ruiz & Licea, 1995 accepted as Synedra capitulata Castracane, 1886
• Thalassionema nitzschioides var. claviformis (Schrader) Moreno in Moreno-Ruiz & Carreno, 1993 accepted as Thalassionema claviformis Schrader, 1973
• Thalassionema nitzschioides var. curvata (Castracane) Mereschkowsky, 1902 accepted as Thalassiothrix curvata Castracane, 1886
• Thalassionema nitzschioides var. curvatum Mereschkowsky, 1902 (uncertain > unassessed)
• Thalassionema nitzschioides var. gracilis Heiden & Kolbe, 1928 (uncertain > unassessed)
• Thalassionema nitzschioides var. incurvata Heiden & Kolbe, 1928 (uncertain > unassessed)
• Thalassionema nitzschioides var. inflata Heiden & Kolbe, 1928 (uncertain > unassessed)
• Thalassionema nitzschioides var. irregulare Jurilj, 1957 (uncertain > unassessed)
• Thalassionema nitzschioides var. javanica (Grunow in Van Heurck) Peragallo & Peragallo, 1901 accepted as Thalassiothrix nitzschioides var. javanica Grunow in Van Heurck, 1881
• Thalassionema nitzschioides var. javanicum (Grunow) Heiden in Heiden & Kolbe, 1928 accepted as Thalassiothrix nitzschioides var. javanica Grunow in Van Heurck, 1881
• Thalassionema nitzschioides var. lanceolata (Grunow in Van Heurck) Peragallo & Peragallo, 1901 accepted as Thalassiothrix nitzschioides var. lanceolata Grunow in Van Heurck, 1881
• Thalassionema nitzschioides var. lanceolatum Grunow, 1928 (uncertain > unassessed)
• Thalassionema nitzschioides var. obtusa (Grunow in Van Heurck) M. Peragallo, 1903 accepted as Thalassiothrix nitzschioides var. obtusa Grunow in Van Heurck, 1881
• Thalassionema nitzschioides var. obtusum (Grunow) Heiden in Heiden & Kolbe, 1928 accepted as Thalassiothrix nitzschioides var. obtusa Grunow in Van Heurck, 1881
• Thalassionema nitzschioides var. parva (Heiden) emend Moreno-Ruiz in Moreno-Ruiz & Licea, 1995 (uncertain > unassessed)
• Thalassionema nitzschioides var. parva Heiden & Kolbe, 1928 (uncertain > unassessed)
• Thalassionema nitzschioides var. robusta Schrader emend Moreno-Ruiz in Moreno-Ruiz & Licea, 1995 (uncertain > unassessed)
• Thalassionema nitzschioides var. schraderi (Akiba) Moreno-Ruiz in Moreno-Ruiz & Licea, 1995 accepted as Thalassionema schraderi Akiba, 1982
• Thalassionema obtusa (Grunow) Andrews, 1976 accepted as Thalassiothrix nitzschioides var. obtusa Grunow in Van Heurck, 1881
• Thalassionema pseudonitzschioides (Schuette & Schrader) Hasle in Hasle & Syvertsen, 1996 accepted as Thalassiothrix pseudonitzschioides G.Schuette & H.Schrader, 1982
• Thalassionema robusta Schrader, 1973 (uncertain > unassessed)
• Thalassionema schraderi Akiba, 1982 (uncertain > unassessed)
• Thalassionema synedriforme (Greville) Hasle, 1999 (uncertain > unassessed)
• Thalassionemataceae Round, 1990
• Thalassionematales