| Hypoxylon aeruginosum var. aeruginosum J. H. Mill., 1933 |
| Hypoxylon aeruginosum var. macrosporum J. D. Rogers, 1985 |
| Hypoxylon albostigmatosum Speg., 1884 |
| Hypoxylon anomalum J.D. Rogers, Y.M. Ju & Oses, 2005 |
| Hypoxylon anthochroum Berk. & Broome, 1873 |
| Hypoxylon archeri Berk., 1859 |
| Hypoxylon berteroi (Mont.) Mont., 1850 |
| Hypoxylon bovei Speg., 1888 |
| Hypoxylon bovei var. bovei Speg., 1888 |
| Hypoxylon bovei var. microsporum J. H. Mill., 1961 |
| Hypoxylon cinnabarinum (Henn.) Y. M. Ju & J. D. Rogers, 1996 |
| Hypoxylon cohaerens (Pers.) Fr., 1849 |
| Hypoxylon cohaerens var. cohaerens (Pers.) Fr., 1849 |
| Hypoxylon comedens Ces., 1879 |
| Hypoxylon conostomum (Mont.) Mont., 1855 |
| Hypoxylon crocopeplum Berk. & M. A. Curtis, 1875 |
| Hypoxylon dieckmannii Theiss., 1908 |
| Hypoxylon duranii J. D. Rogers, 1985 |
| Hypoxylon erythrostroma J. H. Mill., 1933 |
| Hypoxylon fendleri Berk. ex Cooke, 1883 |