• Gomphosphaeria Kützing, 1836
• Gomphosphaeria aponina Kützing, 1836
• Gomphosphaeria botrys Skuja, 1964 accepted as Woronichinia botrys (Skuja) Komárek & Hindák, 1988
• Gomphosphaeria compacta (Lammermann) Ström, 1923 accepted as Woronichinia compacta (Lemmermann) Komárek & Hindák, 1988
• Gomphosphaeria cordiformis (Wille) Hansgirg, 1886
• Gomphosphaeria delicatula Skuja, 1964 accepted as Woronichinia delicatula (Skuja) Komárek & Hindák, 1988
• Gomphosphaeria fusca Skuja, 1948 accepted as Woronichinia fusca (Skuja) Komárek & Hindák, 1988
• Gomphosphaeria gessneri Schiller, 1956
• Gomphosphaeria lacustris Chodat, 1898 accepted as Snowella lacustris (Chodat) Komárek & Hindák, 1988
• Gomphosphaeria lilacea Virieux, 1916
• Gomphosphaeria litoralis Häyrén, 1921 accepted as Snowella litoralis (Häyrén) Komárek & Hindák, 1988
• Gomphosphaeria multiplex (Nygaard) Komárek, 1989
• Gomphosphaeria naegeliana (Unger) Lemmermann, 1907 accepted as Woronichinia naegeliana (Unger) Elenkin, 1933
• Gomphosphaeria natans Komárek & Hindák, 1988
• Gomphosphaeria okavango J. Komárek & G. Cronberg
• Gomphosphaeria okawangae Komárek & Cronberg, 1999
• Gomphosphaeria pusilla (van Goor) Komárek, 1958 accepted as Coelomoron pusillum (Van Goor) Komárek, 1988
• Gomphosphaeria radians Hortobágyi, 1957 accepted as Woronichinia radians (Hortobágyi) Komárek & Hindák, 1988
• Gomphosphaeria robusta Skuja, 1964 accepted as Woronichinia robusta (Skuja) Komárek & Hindák, 1988
• Gomphosphaeria rosea (Snow.) Lemmermann accepted as Snowella rosea (Snow) Elenkin, 1938
• Gomphosphaeria salina Komárek & Hindák, 1988
• Gomphosphaeria semenvitis Komárek, 1989
• Gomphosphaeria tenera Skuja, 1964 accepted as Woronichinia tenera (Skuja) Komárek & Hindák, 1988
• Gomphosphaeria virieuxii Komárek & Hindák, 1988
• Gomphosphaeria wichurae (Hilse) Drouet & Daily, 1952
• Gomphosphaeriaceae Elenkin, 1933