The position of the Acipenseriformes varies from one hypothesis to the other. They are the sister of more advanced actinopterygians in Nelson (1969: Acipenseriformes + [[Lepisosteidae + Amia] + Teleostei]]) and in Bemis et al. (1997: Acipenseriformes + [Lepisosteidae + [Amia + Teleostei]]). Molecular studies have produced conflicting results, e.g., Acipenseriformes are the sister of [Lepisosteidae + Amia + Teleostei] in Lê et al. (1993), but the clade [Acipenseriformes + Lepisosteidae + Amia] is the sister of Teleostei in Ventakesh et al. (2001) and Inoue et al. (2003).

Also, while studying the interrelationships of Acipenseriformes, Grande & Bemis (1996) and Bemis et al. (1997) demonstrated the monophyly of Chondrostei sensu Patterson (1982), including the Acipenseriformes and †Birgeria as their sister taxon, and excluding †Saurichthys. This arrangement contradicts other hypothesis about the relationships of these taxa (Gardiner & Schaeffer 1989, Coates 1999).