• Hadropterus Agassiz, 1854 accepted as Percina Haldeman, 1842
• Hyalopterus Koch, 1854
• Hybopterus Fairmaire, 1883 accepted as Aploscelis Dejean, 1835
• Hydrocherus Cuvier, 1829 accepted as Hydrochoerus Brisson, 1762
• Hydrophorus Battara ex F.S. Earle, 1909 accepted as Hygrocybe (E.M. Fries) P. Kummer, 1871 [Family: Hygrophoraceae]
• Hydrophorus Fallén, 1823 [Family: Dolichopodidae]
• Hydroporus Schellenberg, 1806
• Hydropteris G.W. Rothwell & R.A. Stockey, 1994 † accepted as Hydropteridium A.B. Doweld, 2001 † [Phylum: Tracheophyta]
• Hydropteris L.I. Kondinskaja in A.F. Chlonova, 1966 † [Phylum: Sporae dispersae]
• Hydropyrus Cresson, 1934 (uncertain)
• Hypopterus Gill, 1861 [Family: Latidae]
• Hypopterus Paetel, 1875 (unaccepted) [Family: Mollusca (awaiting allocation)]