• Hypoxylon Adanson, 1763 accepted as Xylaria Hill ex Schrank, 1789 [Phylum: Ascomycota]
• Hypoxylon Bulliard, 1791 [Phylum: Ascomycota]
• Hypoxylon Mérat, 1821 (unaccepted) [Phylum: Fungi (awaiting allocation)]
• Hypoxylon abyssinicum Sacc., 1912 accepted as Kretzschmaria micropus (Fr.) Sacc., 1883
• Hypoxylon adumbratio P.M.D. Martin, 1968 accepted as Nemania bipapillata (Berk. & M.A. Curtis) Pouzar, 1985
• Hypoxylon adumbratio P.M.D. Martin, 1976 accepted as Nemania bipapillata (Berk. & M.A. Curtis) Pouzar, 1985
• Hypoxylon aeneum Nitschke, 1867 accepted as Nemania aenea (Nitschke) Pouzar, 1985
• Hypoxylon aeruginosum J.H. Mill., 1933
• Hypoxylon africanum Van der Byl, 1928 accepted as Hypoxylon thouarsianum (Lév.) Lloyd, 1919
• Hypoxylon aggregatum Welw. & Curr., 1867 accepted as Kretzschmaria micropus (Fr.) Sacc., 1883
• Hypoxylon albocinctum Ellis & Everh., 1890 accepted as Nemania albocincta (Ellis & Everh.) Pouzar, 1985
• Hypoxylon albostigmatosum Speg., 1884 accepted as Hypoxylon anthochroum Berk. & Broome, 1873
• Hypoxylon albotectum Rehm, 1906 accepted as Hypoxylon michelianum Ces. & De Not., 1863
• Hypoxylon amaniense Henn., 1905 accepted as Hypoxylon thouarsianum (Lév.) Lloyd, 1919
• Hypoxylon angolense Welw. & Curr., 1867 accepted as Rhopalostroma angolense (Welw. & Curr.) D. Hawksw., 1977
• Hypoxylon angustum Petch, 1924 accepted as Nemania angusta (Petch) Y.M. Ju & J.D. Rogers, 2002
• Hypoxylon annulatum (Schwein.) Mont., 1850
• Hypoxylon anthochroum Berk. & Broome, 1873
• Hypoxylon anthracoderma Speg., 1888 accepted as Hypoxylon monticulosum Mont., 1856
• Hypoxylon aquilum (Fr.) Bref., 1891 accepted as Rosellinia aquila (Fr.) Ces. & De Not., 1844
• Hypoxylon archeri Berk., 1860
• Hypoxylon areolatum Berk. & M.A. Curtis, 1868 accepted as Hypoxylon bovei Speg., 1887
• Hypoxylon areolatum Starbäck, 1905 accepted as Hypoxylon placentiforme Berk. & M.A. Curtis, 1868
• Hypoxylon argillaceum (Fr.) J. Kickx f., 1835 accepted as Hypoxylon fragiforme (Pers.) J. Kickx f., 1835
• Hypoxylon argillaceum (Pers.) Nitschke, 1867 accepted as Hypoxylon intermedium (Schwein.) Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon asarcodes (Theiss.) J.H. Mill. ex Teng, 1939 accepted as Biscogniauxia capnodes (Berk.) Y.M. Ju & J.D. Rogers, 1998
• Hypoxylon atropunctatum (Schwein.) Cooke, 1883 accepted as Biscogniauxia atropunctata (Schwein.) Pouzar, 1979
• Hypoxylon atropurpureum (Fr.) Fr., 1849 accepted as Nemania atropurpurea (Fr.) Pouzar, 1985
• Hypoxylon atroroseum J.D. Rogers, 1981
• Hypoxylon atrorufum Ellis & Everh., 1892 accepted as Hypoxylon cohaerens (Pers.) Fr., 1849
• Hypoxylon aucklandiae Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon aureostroma P.M.D. Martin, 1969 accepted as Hypoxylon ochraceum Henn., 1897
• Hypoxylon aureostroma P.M.D. Martin, 1976 accepted as Hypoxylon ochraceum Henn., 1897
• Hypoxylon bagnisii Sacc., 1878 accepted as Hypoxylon cohaerens (Pers.) Fr., 1849
• Hypoxylon baileyi Berk. & Broome ex Cooke, 1883 accepted as Biscogniauxia baileyi (Berk. & Broome ex Cooke) Kuntze, 1891
• Hypoxylon bakeri Earle, 1899 accepted as Hypoxylon monticulosum Mont., 1856
• Hypoxylon balansae Speg., 1888 accepted as Nemania caries (Schwein.) Y.M. Ju & J.D. Rogers, 2002
• Hypoxylon bartholomaei Peck, 1911 accepted as Biscogniauxia bartholomaei (Peck) Lar.N. Vassiljeva, 1988
• Hypoxylon beaumontii Berk. & M.A. Curtis, 1876 accepted as Nemania beaumontii (Berk. & M.A. Curtis) Y.M. Ju & J.D. Rogers, 2002
• Hypoxylon begae Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon berberidis (Pers.) J. Kickx f., 1841 accepted as Cucurbitaria berberidis (Pers.) Grev., 1821
• Hypoxylon berkeleyi Sacc., 1883 accepted as Hypoxylon monticulosum Mont., 1856
• Hypoxylon bicolor Ellis & Everh., 1886 accepted as Hypoxylon fuscum (Pers.) Fr., 1849
• Hypoxylon bicoloratum P.M.D. Martin, 1967 accepted as Hypoxylon fuscum (Pers.) Fr., 1849
• Hypoxylon bicoloratum P.M.D. Martin, 1976 accepted as Hypoxylon fuscum (Pers.) Fr., 1849
• Hypoxylon bifrons De Not., 1863 accepted as Creosphaeria sassafras (Schwein.) Y.M. Ju, F. San Martín & J.D. Rogers, 1993
• Hypoxylon bipapillatum Berk. & M.A. Curtis, 1853 accepted as Nemania bipapillata (Berk. & M.A. Curtis) Pouzar, 1985
• Hypoxylon blakei Berk. & M.A. Curtis, 1875 accepted as Entoleuca mammata (Wahlenb.) J.D. Rogers & Y.M. Ju, 1996
• Hypoxylon bogoriense Höhn., 1909 accepted as Hypoxylon stygium (Lév.) Sacc., 1882
• Hypoxylon botrys Nitschke, 1867 accepted as Hypoxylon rubiginosum (Pers.) Fr., 1849
• Hypoxylon bovei Speg., 1887
• Hypoxylon brevirimum Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon brevisporum Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon bulbosa (Pers.) Rabenh., 1844 accepted as Xylaria bulbosa (Pers.) Berk. & Broome, 1860
• Hypoxylon bullatum (Hoffm.) Westend. & Wallays, 1850 accepted as Diatrype bullata (Hoffm.) Fr., 1849
• Hypoxylon bunodes (Berk. & Broome) P.M.D. Martin, 1967 accepted as Rosellinia bunodes (Berk. & Broome) Sacc., 1882
• Hypoxylon bunodes (Berk. & Broome) P.M.D. Martin, 1976 accepted as Rosellinia bunodes (Berk. & Broome) Sacc., 1882
• Hypoxylon caaguazu Speg., 1884 accepted as Hypoxylon subgilvum Berk. & Broome, 1873
• Hypoxylon californicum Ellis & Everh., 1895
• Hypoxylon callimorphum (P. Karst.) P.M.D. Martin, 1967 accepted as Hypoxylon multiforme (Fr.) Fr., 1849
• Hypoxylon callimorphum (P. Karst.) P.M.D. Martin, 1976 accepted as Hypoxylon multiforme (Fr.) Fr., 1849
• Hypoxylon callostroma (Schwein.) Berk., 1875 accepted as Creosphaeria sassafras (Schwein.) Y.M. Ju, F. San Martín & J.D. Rogers, 1993
• Hypoxylon capnodes (Berk.) Berk. & Broome ex Cooke, 1883 accepted as Biscogniauxia capnodes (Berk.) Y.M. Ju & J.D. Rogers, 1998
• Hypoxylon carbonaceum (Pouzar) L.E. Petrini & J.D. Rogers, 1986 accepted as Nemania carbonacea Pouzar, 1985
• Hypoxylon caries (Schwein.) Sacc., 1882 accepted as Nemania caries (Schwein.) Y.M. Ju & J.D. Rogers, 2002
• Hypoxylon carneum Petch, 1924
• Hypoxylon carpini (Pers.) Westend., 1854 accepted as Diaporthe carpini (Pers.) Fuckel, 1870
• Hypoxylon carpophilum (Pers.) Link, 1833 accepted as Xylaria carpophila (Pers.) Fr., 1849
• Hypoxylon catalpae (Schwein.) Sacc., 1882 accepted as Hypoxylon perforatum (Schwein.) Fr., 1849
• Hypoxylon ceratospermum (Tode) J. Kickx f., 1835 accepted as Valsa ceratosperma (Tode) Maire, 1937
• Hypoxylon cercidicola (Berk. & M.A. Curtis ex Peck) Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon cerebrinum (Fée) Cooke, 1883 accepted as Neohypodiscus cerebrinus (Fée) J.D. Rogers, Y.M. Ju & Laessøe, 1994
• Hypoxylon cetrarioides Welw. & Curr., 1867 accepted as Kretzschmaria cetrarioides (Welw. & Curr.) Sacc., 1883
• Hypoxylon chalybaeum Berk. & Broome, 1873 accepted as Hypoxylon nitens (Ces.) Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon chathamense Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon chestersii J.D. Rogers & Whalley, 1978 accepted as Nemania chestersii (J.D. Rogers & Whalley) Pouzar, 1985
• Hypoxylon chionostomum (Speg.) Speg., 1889
• Hypoxylon chrysoconium Berk. & Broome, 1873 accepted as Nemania chrysoconia (Schwein.) Y.M. Ju & J.D. Rogers, 2002
• Hypoxylon cinereolilacinum J.H. Mill., 1933 accepted as Biscogniauxia cinereolilacina (J.H. Mill.) Pouzar, 1979
• Hypoxylon cinereum Ellis & Everh., 1892 accepted as Jumillera cinerea (Ellis & Everh.) J.D. Rogers, Y.M. Ju & F. San Martín, 1997
• Hypoxylon cinnabarinum (Henn.) Y.M. Ju & J.D. Rogers, 1996
• Hypoxylon circostomum Speg., 1921 accepted as Nemania circostoma (Schwein.) Y.M. Ju & J.D. Rogers, 2002
• Hypoxylon circumscribum Lloyd, 1924 accepted as Hypoxylon annulatum (Schwein.) Mont., 1850
• Hypoxylon citriforme Whalley, Hammelev & Talig., 1988 accepted as Biscogniauxia citriformis (Whalley, Hammelev & Talig.) Van der Gucht & Whalley, 1992
• Hypoxylon clavus (Fr.) Mont., 1840 accepted as Kretzschmaria clavus (Fr.) Sacc., 1883
• Hypoxylon clypeus (Schwein.) M.A. Curtis, 1867 accepted as Biscogniauxia mediterranea (De Not.) Kuntze, 1891
• Hypoxylon coccinellum Sacc., 1913 accepted as Hypoxylon howeanum Peck, 1872
• Hypoxylon coccineum Bull., 1791 accepted as Hypoxylon fragiforme (Pers.) J. Kickx f., 1835
• Hypoxylon coccineum sensu Plowright (1875) accepted as Hypoxylon howeanum Peck, 1872
• Hypoxylon coenopus (Fr.) Mont., 1840 accepted as Kretzschmaria clavus (Fr.) Sacc., 1883
• Hypoxylon cohaerens (Pers.) Fr., 1849
• Hypoxylon colliculosum (Schwein.) Nitschke, 1867 accepted as Nemania serpens (Pers.) Gray, 1821
• Hypoxylon commutatum Nitschke, 1867
• Hypoxylon compunctum (Jungh.) Fr., 1851 accepted as Penzigia compuncta (Jungh.) Sacc. & Paol., 1888
• Hypoxylon concentricum (Bolton) Grev., 1828 accepted as Daldinia concentrica (Bolton) Ces. & De Not., 1863
• Hypoxylon concurrens Berk. & M.A. Curtis, 1876 accepted as Hypoxylon investiens (Schwein.) M.A. Curtis, 1867
• Hypoxylon confluens (Tode) Westend., 1845 accepted as Nemania confluens (Tode) Læssøe & Spooner, 1994
• Hypoxylon confluens (Willd.) Wettst., 1885 accepted as Hypoxylon fuscum (Pers.) Fr., 1849
• Hypoxylon congoanum Torrend ex Beeli, 1923 accepted as Hypoxylon subrutilum Starbäck, 1901
• Hypoxylon congoense Sacc., 1906 accepted as Hypoxylon placentiforme Berk. & M.A. Curtis, 1868