 Hypacrosaurus was a lambeosaurine hadrosaurid, and has been recognized as such since the description of its skull. Within the Lambeosaurinae, it is closest to Lambeosaurus and Corythosaurus, with Jack Horner and Phil Currie (1994) suggesting that H. stebingeri is transitional between Lambeosaurus and H. altispinus, and Michael K. Brett-Surman (1989) suggesting that Hypacrosaurus and Corythosaurus are the same genus. These genera, particularly Corythosaurus and Hypacrosaurus, are regarded as the "helmeted" or "hooded" branch of the lambeosaurines, and the clade they form is sometimes informally designated Lambeosaurini. Although Suzuki et al. ' s 2004 redescription of Nipponosaurus found a close relationship between Nipponosaurus and Hypacrosaurus stebingeri, indicating that Hypacrosaurus may be paraphyletic, this was rejected in a later, more comprehensive reanalysis of lambeosaurines, which found the two species of Hypacrosaurus to form a clade without Nipponosaurus, with Corythosaurus and Olorotitan being the closest relatives.
