Allokotosauria was first described and named when a new monophyletic grouping of specialized herbivorous archosauromorphs was recovered by Sterling J. Nesbitt, John J. Flynn, Adam C. Pritchard, J. Michael Parrish, Lovasoa Ranivoharimanana and André R. Wyss in 2015.

The name Allokotosauria is derived from Greek meaning "strange reptiles" in reference to unexpected grouping of early archosauromorph with a high disparity of features typically associated with herbivory.

Nesbitt et al. (2015) defined the group as a stem-based taxon containing Azendohsaurus madagaskarensis and Trilophosaurus buettneri and all taxa more closely related to them than to Tanystropheus longobardicus, Proterosuchus fergusi, Protorosaurus speneri or Rhynchosaurus articeps.

[5] Choristodera Aenigmastropheus Protorosaurus Prolacertoides Jesairosaurus Tanystropheidae Teraterpeton hrynewichorum Trilophosaurus buettneri Spinosuchus caseanus (= "Trilophosaurus" jacobsi) Pamelaria dolichotrachela Shringasaurus indicus Azendohsaurus laaroussii Azendohsaurus madagaskarensis Rhynchosauria Boreopricea Prolacertidae Tasmaniosaurus Archosauriformes Pritchard and Nesbitt (2017) found support for the inclusion of Kuehneosauridae within Allokotosauria.

[7] Malerisaurus robinsonae Azendohsaurus madagaskarensis Pamelaria dolichotrachela Teraterpeton hrynewichorum Spinosuchus caseanus Trilophosaurus buettneri Avicranium renestoi Hypuronector limnaios Vallesaurus cenensis Dolabrosaurus aquatilis Drepanosaurus unguicaudatus Megalancosaurus preonensis