Anisodontosaurus greeri is an enigmatic small-bodied tetrapod with a heterodont dentition from the Holbrook Member of the Moenkopi Formation (Middle Triassic) of Arizona (U.S.A.). The evolutionary relationships of this taxon have long been debated and remain uncertain. Using micro-computed tomography (µCT) scans we redescribe the holotype of Anisodontosaurus greeri (UCMP 37804), as well as an additional specimen (MNA.V.1478) that had been informally referred to this taxon. Our new data reveal hidden details of the dentition (i.e., ankylothecodonty and absence of replacement teeth) that, in combination with the tricuspid and mediolaterally expanded crowns, support a referral of both specimens to the archosauromorph clade Trilophosauridae. The referral of MNA.V.1478 to Anisodontosaurus greeri is supported by the unique anatomy of the highly differentiated dentition (i.e., ‘figure of 8’-shaped premolariforms in occlusal views; mesiodistally short tooth row; presence of a distal ‘molariform’ crown). Comparison of Anisodontosaurus greeri with other trilophosaurids highlights marked similarities with Variodens inopinatus from the Upper Triassic deposits of the U.K. Our cladistic analyses confirm these observations, and recover, for the first time, two distinct lineages within Trilophosauridae: one geologically long-lived and comprising Anisodontosaurus and Variodens; and one comprising Tricuspisaurus, Trilophosaurus spp., and Spinosuchus. These results imply that: (i) Anisodontosaurus is one of the oldest known trilophosaurids worldwide and the oldest in North America; (ii) trilophosaurids achieved a broad distribution at low latitudes within western Pangea by the Middle Triassic; (iii) small body sizes were more common than previously thought among trilophosaurids.