| Hypotrachyna lividescens (Kurok.) Hale, 1974 |
| Hypotrachyna longiloba (H. Magn.) C.W. Sm., 1993 |
| Hypotrachyna meridensis Hale & López-Fig., 1979 |
| Hypotrachyna mexicana (Egan) Divakar, A. Crespo, Sipman, Elix & Lumbsch, 2013 |
| Hypotrachyna microblasta (Vain.) Hale, 1975 |
| Hypotrachyna minarum (Vain.) Krog & Swinscow, 1987 |
| Hypotrachyna neocirrhata (Hale & M. Wirth) Divakar, A. Crespo, Sipman, Elix & Lumbsch, 2013 |
| Hypotrachyna neodissecta (Hale) Hale, 1975 |
| Hypotrachyna nepalensis (Taylor) Divakar, A. Crespo, Sipman, Elix & Lumbsch, 2013 |
| Hypotrachyna nigrociliata (B. de Lesd.) Divakar, A. Crespo, Sipman, Elix & Lumbsch, 2013 |
| Hypotrachyna osseoalba (Vain.) Y.S.Park& Hale, 1989 |
| Hypotrachyna partita Hale, 1975 |
| Hypotrachyna physcioides (Nyl.) Hale, 1975 |
| Hypotrachyna pluriformis (Nyl.) Hale, 1975 |
| Hypotrachyna prolongata (Kurok.) Hale, 1975 |
| Hypotrachyna protenta Hale, 1975 |
| Hypotrachyna pseudonepalensis (Hale & M. Wirth) Divakar, A. Crespo, Sipman, Elix & Lumbsch, 2013 |
| Hypotrachyna pseudosinuosa (Asahina) Hale, 1975 |
| Hypotrachyna pulvinata (Fée) Hale, 1975 |
| Hypotrachyna pustulifera (Hale) Skorepa, 1983 |