Gasterosteoidei is treated as a suborder within the order Scorpaeniformes in the 5th edition of Fishes of the World,[2] but in other phylogenetic classifications it is treated as the infraorder Gasterosteales within the suborder Cottoidei or as a sister clade to the Zoarcales in the order Zoarciformes.

[3] Indostomidae is included within Gasterosteoidei in Fishes of the World'[2] but according to Betancur et al its inclusion in the clade renders it paraphyletic and they classify that family within the monotypic suborder Indostomoidei within the Synbranchiformes.

The more typical members of that group (e.g. scorpionfishes) are apparently closer to the "true" Gasterosteiformes, whereas the keel-bodied flying gurnards (Dactylopteridae) seem actually to belong to the Syngnathiformes clade.

It seems that the closest living relatives of the narrowly delimited Gasterosteoidei are the Zoarcoidei, which have been placed in the massively paraphyletic "Perciformes".

The kidneys of gasterosteoids synthesis an adhesive chemical which is used by males to create nests of plant material, it is not known if this is true of all the taxa within the group.