• Gnatholepis Bleeker, 1874
• Gnatholepis anjerensis (Bleeker, 1851)
• Gnatholepis argus Larson & Buckle, 2005
• Gnatholepis australis Randall & Greenfield, 2001 accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis baliurus (Valenciennes, 1837) accepted as Arcygobius baliurus (Valenciennes, 1837)
• Gnatholepis calliurus Jordan & Seale, 1905 accepted as Arcygobius baliurus (Valenciennes, 1837)
• Gnatholepis caudimaculata Larson & Buckle, 2012
• Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis cauerensis australis Randall & Greenfield, 2001 accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis cauerensis cauerensis (Bleeker, 1853) accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis cauerensis hawaiiensis Randall & Greenfield, 2001 accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis cauerensis pascuensis Randall & Greenfield, 2001 accepted as Gnatholepis pascuensis Randall & Greenfield, 2001
• Gnatholepis corlettei Herre, 1935 accepted as Gnatholepis ophthalmotaenia (Bleeker, 1854)
• Gnatholepis davaoensis Seale, 1910 accepted as Gnatholepis ophthalmotaenia (Bleeker, 1854)
• Gnatholepis deltoides (Seale, 1901) accepted as Gnatholepis anjerensis (Bleeker, 1851)
• Gnatholepis gemmeus Herre, 1927 accepted as Gnatholepis ophthalmotaenia (Bleeker, 1854)
• Gnatholepis gymnocara Randall & Greenfield, 2001
• Gnatholepis hawaiiensis Randall & Greenfield, 2001 accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis hendersoni Herre, 1936 accepted as Macrodontogobius wilburi Herre, 1936
• Gnatholepis hololepis Schultz, 1943 accepted as Macrodontogobius wilburi Herre, 1936
• Gnatholepis inconsequens Whitley, 1958 accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis knighti Jordan & Evermann, 1903
• Gnatholepis knightii Jordan & Evermann, 1903 accepted as Gnatholepis anjerensis (Bleeker, 1851)
• Gnatholepis koumansi Herre, 1937 accepted as Aulopareia koumansi (Herre, 1937)
• Gnatholepis mingi Herre, 1936 accepted as Hemigobius mingi (Herre, 1936)
• Gnatholepis ophthalmotaenia (Bleeker, 1854)
• Gnatholepis pascuensis Randall & Greenfield, 2001
• Gnatholepis puntangoides (Bleeker, 1854) accepted as Exyrias puntang (Bleeker, 1851)
• Gnatholepis scapulostigma Herre, 1953 accepted as Gnatholepis cauerensis (Bleeker, 1853)
• Gnatholepis sindonis Snyder, 1908 accepted as Exyrias puntang (Bleeker, 1851)
• Gnatholepis thompsoni Jordan, 1904
• Gnatholepis thomsoni Jordan, 1904 accepted as Gnatholepis thompsoni Jordan, 1904
• Gnatholepis volcanus Herre, 1927 accepted as Exyrias volcanus (Herre, 1927)
• Gnatholepis yoshinoi Suzuki & Randall, 2009