| Encyonema lange-bertalotii Krammer, 1997 |
| Encyonema leibleinii (C. Agardh) Silva, Jahn, Ludwig & Menezes, 2013 |
| Encyonema lunatum (W. Sm.) Van Heurck, 1880 |
| Encyonema mesianum (Cholnoky) D.G. Mann, 1990 |
| Encyonema mexicanum Krammer, 1997 |
| Encyonema minutiforme Krammer, 1997 |
| Encyonema minutum (Hilse) D.G. Mann, 1990 |
| Encyonema muelleri (Hustedt) D.G. Mann, 1990 |
| Encyonema neogracile Krammer, 1997 |
| Encyonema neosubturgidum (Hust., 1942) Da Silva & M. Menezes, 2016 |
| Encyonema norvegicum (Grunow) Mayer, 1947 |
| Encyonema pergracile Krammer, 1997 |
| Encyonema perminutum Krammer, 1997 |
| Encyonema perpusillum (A. Cleve) D.G. Mann, 1990 |
| Encyonema polystigmoideum Metzeltin & Krammer, 1998 |
| Encyonema prostratum (Berk.) Kütz., 1844 |
| Encyonema rumrichae Krammer, 1997 |
| Encyonema silesiacum (Bleisch) D.G. Mann, 1990 |
| Encyonema subelginense Krammer, 1997 |
| Encyonema triangulum (Ehrenb.) Kütz., 1849 |