• Protocystiphyllum He, 1978 † (uncertain)
• Protocystis Bather in Lankester, 1900 † [Family: Rhombifera (awaiting allocation)]
• Protocystis Wallich, 1862 [Family: Challengeriidae]
• Protocystis harstoni (Murray, 1885)
• Protocystis tridens (Haeckel, 1887) accepted as Protocystis tridens Bjørklund, 1976
• Protocystis tridens Bjørklund, 1976
• Protocystis xiphodon Haeckel, 1862
• Protocystites Hicks, 1872 †
• Protocystites Salter, 1866 † accepted as Protocystites Hicks, 1872 †