| 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 |
| Encyclia favoris (Rchb. f.) Soto Arenas, 1988 |
| Encyclia flabellata (Lindl.) B.F. Thurston & W.R. Thurston, 1977 |
| Encyclia fragrans (Sw.) Lemée, 1955 |
| Encyclia ghiesbreghtiana (A. Rich. & Galeotti) Dressler, 1961 |
| Encyclia glauca (Knowles & Westc.) Dressler & G.E. Pollard, 1971 |
| Encyclia gravida (Lindl.) Schltr., 1918 |
| Encyclia greenwoodiana Ag.-Olav., 1992 |
| Encyclia guadalupeae R. González & Alvarado, 1999 |
| Encyclia guatemalensis (Klotzsch) Dressler & G.E. Pollard, 1971 |
| Encyclia guttata Schltr., 1918 |
| Encyclia halbingeriana Hágsater & Soto Arenas, 2008 |
| Encyclia hanburyi (Lindl.) Schltr., 1914 |
| Encyclia hastata (Lindl.) Dressler & G.E. Pollard, 1971 |
| Encyclia huertae Soto Arenas & R. Jiménez, 2003 |