| Hypoxylon rosellinoides Henn., 1905 |
| Hypoxylon rubigineoareolatum Rehm, 1908 |
| Hypoxylon rubiginosum (Pers.) Fr., 1849 |
| Hypoxylon rubiginosum var. rubiginosum (Pers.) Fr., 1849 |
| Hypoxylon rubiginosum var. tropicum J. H. Mill., 1961 |
| Hypoxylon sclerophaeum Berk. & M. A. Curtis, 1854 |
| Hypoxylon semimultiforme F. San Martín, P. Lavín & Pérez-Silva, 1999 |
| Hypoxylon shearii Y. M. Ju & J. D. Rogers, 1996 |
| Hypoxylon shearii var. minor F. San Martín, Y. M. Ju & J. D. Rogers, 1999 |
| Hypoxylon shearii var. shearii Y. M. Ju & J. D. Rogers, 1996 |
| Hypoxylon stygium (Lév.) Sacc., 1882 |
| Hypoxylon subgilvum Berk. & Broome, 1873 |
| Hypoxylon subrutilum Starbäck, 1901 |
| Hypoxylon sulcatum Starbäck, 1904 |
| Hypoxylon symphyon Möller, 1901 |
| Hypoxylon texcalense F. San Martín, Port.-Port. & P. Lavín, 1999 |
| Hypoxylon thouarsianum (Lév.) Lloyd, 1919 |
| Hypoxylon thouarsianum var. gilletianum (Sacc.) J. H. Mill., 1961 |
| Hypoxylon thouarsianum var. macrosporum F. San Martín, Y. M. Ju & J. D. Rogers, 1996 |
| Hypoxylon thouarsianum var. thouarsianum (Lév.) Lloyd, 1919 |