- Paraphysomonas antarctica Takahashi, 1987
- Paraphysomonas butcheri Pennick & Clarke, 1972 accepted as Lepidochromonas butcheri (Pennick & K.J.Clarke) Kapustin & Guiry, 2019
- Paraphysomonas cribosa I.A.N.Lucas, 1968 accepted as Lepidochromonas cribosa (I.A.N.Lucas) Kapustin & Guiry, 2019
- Paraphysomonas cylicophora Leadbeater, 1972
- Paraphysomonas cyliophora Leadbeater, 1972 accepted as Paraphysomonas cylicophora Leadbeater, 1972
- Paraphysomonas imperforata I.A.N.Lucas, 1967
- Paraphysomonas oligocycla Takahashi, 1987
- Paraphysomonas vestita (A.C.Stokes) De Saedeleer, 1930