| Encyclia chondylobulbon (A. Rich. & Galeotti) Dressler, 1971 |
| Encyclia citrina (Lex.) Dressler, 1961 |
| Encyclia cochleata (L.) Lemée, 1955 |
| Encyclia cochleata subsp. triandra (Ames) Hágsater, 1994 |
| Encyclia concolor (Lex.) Schltr., 1918 |
| Encyclia contrerasii R. González, 1997 |
| Encyclia cordigera (Kunth) Dressler, 1964 |
| Encyclia cordigera var. rosea (Bateman) H.G. Jones, 1969 |
| Encyclia cretacea Dressler & G.E. Pollard, 1971 |
| Encyclia cyanocolumna (Ames, F.T. Hubb. & C. Schweinf.) Dressler, 1961 |
| Encyclia deamii (Schltr.) Hoehne, 1952 |
| Encyclia dickinsoniana (Withner) Hamer, 1985 |
| Encyclia diguetii (Ames) Hoehne, 1952 |
| Encyclia diota (Lindl.) Schltr., 1918 |
| Encyclia diota subsp. atrorubens (Rolfe) Dressler & G.E. Pollard, 1971 |
| Encyclia distantiflora (A. Rich. & Galeotti) Dressler & G.E. Pollard, 1971 |
| Encyclia doeringii Hoehne, 1946 |
| Encyclia dressleri Beutelsp. & Moreno-Molina, 2018 |
| Encyclia enriquearcilae Carnevali & Cetzal, 2018 |
| Encyclia erubescens (Lindl.) Schltr., 1914 |