| Encyclia adenocaula (Lex.) Schltr., 1918 |
| Encyclia adenocaula subsp. adenocaula (Lex.) Schltr., 1918 |
| Encyclia adenocaula subsp. kennedyi (Fowlie & Withner) Soto Arenas, Salazar & Hágsater, 2002 |
| Encyclia adenocaula var. kennedyi (Fowlie & Withner) Hágsater & R. González, 1975 |
| Encyclia aenicta Dressler & G.E. Pollard, 1971 |
| Encyclia affinis Schltr., 1918 |
| Encyclia alata (Bateman) Schltr., 1914 |
| Encyclia alata subsp. alata (Bateman) Schltr., 1914 |
| Encyclia alata subsp. parviflora (Regel) Dressler & G.E. Pollard, 1971 |
| Encyclia alata subsp. virella Dressler & G.E. Pollard, 1971 |
| Encyclia alborubra Archila, Chiron & Szlach., 2016 |
| Encyclia amabilis (Linden & Rchb. f.) Schltr., 1918 |
| Encyclia amanda (Ames) Dressler, 1971 |
| Encyclia ambigua (Lindl.) Schltr., 1914 |
| Encyclia aromatica (Bateman) Schltr., 1914 |
| Encyclia asperula Dressler & G.E. Pollard, 1974 |
| Encyclia atropurpurea (Willd.) Schltr., 1914 |
| Encyclia atropurpurea var. leucantha Schltr., 1922 |
| Encyclia atropurpurea var. rhodoglossa Schltr., 1922 |
| Encyclia atropurpurea var. rosea (Bateman) Summerh., 1957 |