• Cystodinium Klebs, 1912
• Cystodinium Schulz & Mai, 1966 † (unaccepted > nomen nudum)
• Cystodinium acerosum R.H. Thompson, 1984
• Cystodinium bataviense Klebs, 1912
• Cystodinium bicorne (Woloszynska) Huber-Pestalozzi, 1950 accepted as Dinococcus bicornis (Woloszynska) Fott, 1960
• Cystodinium brevipes Geitler, 1928 accepted as Dinococcus oedogonii (P. Richter) Fott, 1960
• Cystodinium conchaeforme Baumeister, 1963 accepted as Cystodinium phaseolus Pascher, 1928
• Cystodinium cornifax (Schilling) G.A. Klebs, 1912
• Cystodinium dimorphe (Baumeister) Huber-Pestalozzi, 1950 accepted as Cystodinium phaseolus Pascher, 1928
• Cystodinium dominii Fott, 1933 accepted as Cystodinium phaseolus Pascher, 1928
• Cystodinium gessneri (Baumeister) Bourrelly, 1970 accepted as Gymnodinium fuscum (Ehrenberg) F. Stein, 1878
• Cystodinium hyalinum Pascher, 1944 accepted as Cystodinium phaseolus Pascher, 1928
• Cystodinium iners Geitler, 1928 accepted as Cystodinium cornifax (Schilling) G.A. Klebs, 1912
• Cystodinium lunare Pascher, 1927 accepted as Cystodinium bataviense Klebs, 1912
• Cystodinium minimum Pascher, 1944 accepted as Cystodinium phaseolus Pascher, 1928
• Cystodinium phaseolus Pascher, 1928
• Cystodinium schilleri Baumeister, 1957 accepted as Cystodinium cornifax (Schilling) G.A. Klebs, 1912
• Cystodinium steinii Klebs, 1912 accepted as Cystodinium cornifax (Schilling) G.A. Klebs, 1912
• Cystodinium unicorne Klebs, 1912 accepted as Cystodinium cornifax (Schilling) G.A. Klebs, 1912