"Banksia aquilonia" was first described by Alex George in 1981 as a variety of "Banksia integrifolia" (coast banksia), from a specimen collected at Witts Lookout in Crystal Creek National Park south of Ingham on 12 April 1975. The species name is the Latin adjective "aquilonius", meaning "northern", as it was the most northerly form of "B. integrifolia". In 1996 Kevin Thiele and Pauline Ladiges published a cladistic analysis of "Banksia" based on morphology, in which this taxon stood out as the only member of "B. integrifolia" to be both morphologically and geographically distinct from other infraspecific taxa. They also noted that there were no intermediate plants between what was then known as "B. integrifolia" var. "aquilonia" and other populations of "B. integrifolia". On this basis they would have liked to promote it to species rank, but did not because their inferred phylogeny suggested that this taxon arose from within "B. integrifolia". They were unwilling to render "B. integrifolia" paraphyletic by elevating this taxon to species rank, and they were equally unwilling to elevate all four varieties to species rank, since the others all had significant overlaps in distribution and morphology. Therefore, they simply promoted all four to subspecies rank. This example has since been held up as an interesting case study on how the concept of "species" should be defined, as it presents the problem of "a monophyletic group comprising a paraphyletic basal group of incompletely differentiated geographic forms within which is nested at least one divergent, autapomorphic taxon that invites treatment as a species."