Hypsagoninae was first proposed as a taxonomic grouping in 1861 by the American zoologist Theodore Gill. Some workers have regarded the genus Agonomalus as synonymous with Hypsagonus and place the two remaining genera in the subfamily Percidinae which was also named by Gill in 1897. However, most authorities recognise the three genera and place the in the subfamily Hypsagoninae. The 5th editiuon of Fishes of the World classifies the Hypsagoninae within the family Agonidae, part of the superfamily Cottoidea, the sculpins.
