| Encyonema Kütz., 1834 |
| Encyonema alpinum (Grunow) D.G. Mann, 1990 |
| Encyonema auerswaldii Rabenh., 1853 |
| Encyonema brehmi (Hust.) D.G. Mann, 1990 |
| Encyonema brehmii (Hust.) D.G. Mann, 1990 |
| Encyonema brevicapitatum Krammer, 1997 |
| Encyonema caespitosum Kütz., 1849 |
| Encyonema carina Lange-Bert. & Krammer, 1997 |
| Encyonema cespitosum Kütz., 1849 |
| Encyonema densistriata E. Novelo, R. Tavera & C. Ibarra, 2007 |
| Encyonema dubium Krammer, 1997 |
| Encyonema elginense (Krammer) D.G. Mann, 1990 |
| Encyonema evergladianum Krammer, 1997 |
| Encyonema gaeumannii (Meister) Krammer, 1997 |
| Encyonema gracile Rabenhorst, 1853 |
| Encyonema hebridicum (Gregory) Grunow, 1891 |
| Encyonema hebridiforme Krammer, 1997 |
| Encyonema jemtlandicum Krammer, 1997 |
| Encyonema jemtlandicum var. venezolanum Krammer, 1997 |
| Encyonema lacustre (C. Agardh) F.W.Mills, 1934 |