- Jaaginema angustissimum (West & G.S.West) Anagnostidis & Komárek, 1988
- Jaaginema geminatum (Schwabe ex Gomont) Anagnostidis & Komárek, 1988
- Jaaginema homogeneum (Frémy) Anagnostidis & Komárek, 1988
- Jaaginema lemmermannii (Woloszynska) Anagnostidis & Komárek, 1988 accepted as Anagnostidinema lemmermannii (Wołoszyńska) Strunecky, Bohunická, J.R.Johansen, Capková, Raabová, P.Dvořák & Komárek, 2017
- Jaaginema metaphyticum Komárek, 1988
- Jaaginema subtilissimum (Kützing ex Forti) Anagnostidis & Komárek, 1988