Bothragonus was first proposed as a genus by the American zoologist Theodore Gill in 1883 with Hypsagonus swanii, which had been described in 1876 by Franz Steindachner from Port Townsend on Puget Sound in Washington, as its type species.

[2][3] In 1971 the Soviet ichthyologist Georgii Ustinovich Lindberg proposed that the genus Bothragonus be placed in the new subfamily of the Agonidae, the Bothragoninae, although this was not universally accepted.

[4] The 5th edition of Fishes of the World recognises the validity of the Bothragoninae as a subfamily of the Agonidae.

[5] There are currently two recognized species in this genus:[6] Bothragonus is a combination of bothra, meaning "cavity", a reference to the deep pit on the nape, and Agonus the type genus of the Agonidae.

[6] Bothragonus are found in the eastern and western North Pacific Ocean.