| Hypotrachyna cirrhata Fr., 2013 |
| Hypotrachyna costaricensis (Nyl.) Hale, 1975 |
| Hypotrachyna croceopustulata (Kurok.) Hale, 1975 |
| Hypotrachyna culbersoniorum Elix & T.H. Nash, 2002 |
| Hypotrachyna dactylifera (Vain.) Hale, 1975 |
| Hypotrachyna densirhizinata (Kurok.) Hale, 1975 |
| Hypotrachyna dentella (Hale & Kurok.) Hale, 1975 |
| Hypotrachyna endochlora (Leight.) Hale, 1975 |
| Hypotrachyna ensifolia (Kurok.) Hale, 1975 |
| Hypotrachyna exsplendens (Hale) Hale, 1975 |
| Hypotrachyna flavida (Zahlbr.) Hale, 1975 |
| Hypotrachyna formosana (Zahlbr.) Hale, 1975 |
| Hypotrachyna gondylophora (Hale) Hale, 1975 |
| Hypotrachyna horrescens (Taylor) Krog & Swinscow., 1987 |
| Hypotrachyna imbricatula (Zahlbr.) Hale, 1975 |
| Hypotrachyna immaculata (Kurok.) Hale, 1975 |
| Hypotrachyna isidiocera (Nyl.) Hale, 1975 |
| Hypotrachyna koyaensis (Asahina) Hale, 1975 |
| Hypotrachyna laevigata (Sm.) Hale, 1975 |
| Hypotrachyna lipidifera (Hale & M. Wirth) Divakar, A. Crespo, Sipman, Elix & Lumbsch, 2013 |