Se reconocen los siguientes géneros agrupados en once subfamilias:^[1]​

• Baliphoxus Ortiz & Lalana, 1999
• Indophoxus Dang & Hung Anh Le, 2005
• Linca Alonso de Pina, 1993
• Vietophoxus Dang & Hung Anh Le, 2005
• Subfamilia Birubiinae Barnard & Drummond, 1978
  • Bathybirubius Senna, 2010
  • Birubius Barnard & Drummond, 1976
  • Kulgaphoxus Barnard & Drummond, 1978
  • Phoxorgia Barnard & Barnard, 1980
  • Tickalerus Barnard & Drummond, 1978
  • Yan Barnard & Drummond, 1978
• Subfamilia Brolginae Barnard & Drummond, 1978
  • Brolgus Barnard & Drummond, 1978
  • Cunmurra Barnard & Drummond, 1978
  • Elpeddo Barnard & Drummond, 1978
  • Eobrolgus J.L. Barnard, 1979
  • Eyakia J.L. Barnard, 1979
  • Foxiphalus J.L. Barnard, 1979
  • Fuegiphoxus Barnard & Barnard, 1980
  • Ganba Barnard & Drummond, 1978
  • Kuritus Barnard & Drummond, 1978
  • Mandibulophoxus Barnard, 1957
  • Parafoxiphalus Alonso de Pina, 2001
  • Paramesophoxus Gurjanova, 1977
  • Paraphoxus Sars, 1891
  • Pseudfoxiphalus Andres, 1991
  • Waipirophoxus Gurjanova, 1980
  • Wildus Barnard & Drummond, 1978
• Subfamilia Harpiniinae Barnard & Drummond, 1978
  • Basuto Barnard & Drummond, 1978
  • Cocoharpinia G. Karaman, 1980
  • Coxophoxus Barnard, 1966
  • Feriharpinia Barnard & Karaman, 1982
  • Harpinia Boeck, 1876
  • Harpiniopsis Stephensen, 1925
  • Heterophoxus Shoemaker, 1925
  • Proharpinia Schellenberg, 1931
  • Pseudharpinia Schellenberg, 1931
  • Torridoharpinia Barnard & Karaman, 1982
• Subfamilia Joubellinae Barnard & Drummond, 1978
  • Joubinella Chevreux, 1908
  • Kotla Barnard & Drummond, 1978
  • Matong Barnard & Drummond, 1978
  • Synphoxus Gurjanova, 1980
  • Yammacoona Barnard & Drummond, 1978
• Subfamilia Leongathinae Barnard & Drummond, 1978
  • Leongathus Barnard & Drummond, 1978
• Subfamilia Metharpiniinae Jarrett & Bousfield, 1994
  • Beringiaphoxus Jarrett & Bousfield, 1994
  • Grandifoxus J.L. Barnard, 1979
  • Majoxiphalus Jarrett & Bousfield, 1994
  • Metharpinia Schellenberg, 1931
  • Microphoxus J.L. Barnard, 1960
  • Rhepoxynius J.L. Barnard, 1979
• Subfamilia Palabriaphoxinae Gurjanova, 1977
  • Palabriaphoxus Gurjanova, 1977
• Subfamilia Parharpiniinae Barnard & Drummond, 1978
  • Parharpinia Stebbing, 1899
  • Protophoxus K.H. Barnard, 1930
• Subfamilia Phoxocephalinae G.O. Sars, 1891
  • Cephalophoxoides Gurjanova, 1977
  • Cephalophoxus Gurjanova, 1977
  • Diogodias Barnard & Drummond, 1978
  • Eusyrophoxus Gurjanova, 1977
  • Hopiphoxus Barnard & Drummond, 1978
  • Japara Barnard & Drummond, 1978
  • Jerildaria Barnard & Drummond, 1978
  • Kondoleus Barnard & Drummond, 1978
  • Leptophoxoides Barnard, 1962
  • Leptophoxus G.O. Sars, 1895
  • Limnoporeia Fearn-Wannan, 1968
  • Mesophoxus Gurjanova, 1977
  • Metaphoxoides Ledoyer, 1967
  • Metaphoxus Bonnier, 1896
  • Parajoubinella Gurjanova, 1977
  • Parametaphoxus Jarrett & Bousfield, 1994
  • Phoxocephalus Stebbing, 1888
  • Rikkarus Barnard & Drummond, 1978
  • Ringaringa Barnard & Karaman, 1991
  • Uldanamia Barnard & Drummond, 1978
  • Vasco Barnard & Drummond, 1978
• Subfamilia Pontharpiniinae Barnard & Drummond, 1978
  • Griffithsius Jarrett & Bousfield, 1994
  • Pontharpinia Stebbing, 1897
  • Urophoxus Gurjanova, 1977
• Subfamilia Tipimeginae Barnard & Drummond, 1978
  • Booranus Barnard & Drummond, 1978
  • Tipimegus Barnard & Drummond, 1978
  • Trichophoxus K.H. Barnard, 1930
  • Waitangi Fincham, 1977

•   Wikispecies tiene un artículo sobre Phoxocephalidae.