Caipirasuchus was first named by Fabiano V. Iori and Ismar S. Carvalho in 2011 and the type species is C. paulistanus.
The generic name is derived from Portuguese word Caipira which refers to the rural inhabitants of the Brazilian states, covering almost all of the Bauru Basin, and Greek souchus meaning "crocodile".
The specific name is derived from "paulista", the designation for the residents of São Paulo State, where the holotype was found.

C. paulistanus is known only from the holotype specimen MPMA 67-0001/00, an almost complete and undeformed skull and mandible with teeth (only three teeth are missing) and partial postcranium from a single individual.
It was found on the São Francisco Farm, in Homem de Mello, the rural area of Monte Alto County of northern São Paulo.
It was collected from the Adamantina Formation of the Bauru Basin, which dates to the Turonian and Santonian stages of the Late Cretaceous.

A second species, C. montealtensis, was named by Marco Brandalise de Andrade and Reinaldo J. Bertini in 2008 as a species of the closely related notosuchian genus Sphagesaurus, on the basis of MPMA 15-001/90, a nearly complete skull and mandible preserved in occlusion.
It was collected from the Bairro Cachoeira locality at the base of the Serra da Água Limpa, about 8 km northwest of Monte Alto, from the Adamantina Formation.
In 2013, this specimen was reassigned to Caipirasuchus on the basis of a newly discovered specimen referrable to it.
MPMA 68-0003/12 consists of a nearly complete cranium and mandible, and a posterior portion of the post-cranium.
It was discovered in the municipality of Catanduva, northern São Paulo, from the Adamantina Formation.
At least five synapomorphies unite the species, and a phylogenetic analysis found them to be sister taxa.
Caipirasuchus was first named by Fabiano V. Iori and Ismar S. Carvalho in 2011 and the type species is C. paulistanus. The generic name is derived from Portuguese word Caipira which refers to the rural inhabitants of the Brazilian states, covering almost all of the Bauru Basin, and Greek souchus meaning "crocodile". The specific name is derived from "paulista", the designation for the residents of São Paulo State, where the holotype was found.
C. paulistanus is known only from the holotype specimen MPMA 67-0001/00, an almost complete and undeformed skull and mandible with teeth (only three teeth are missing) and partial postcranium from a single individual. It was found on the São Francisco Farm, in Homem de Mello, the rural area of Monte Alto County of northern São Paulo. It was collected from the Adamantina Formation of the Bauru Basin, which dates to the Turonian and Santonian stages of the Late Cretaceous.
A second species, C. montealtensis, was named by Marco Brandalise de Andrade and Reinaldo J. Bertini in 2008 as a species of the closely related notosuchian genus Sphagesaurus, on the basis of MPMA 15-001/90, a nearly complete skull and mandible preserved in occlusion. It was collected from the Bairro Cachoeira locality at the base of the Serra da Água Limpa, about 8 km northwest of Monte Alto, from the Adamantina Formation. In 2013, this specimen was reassigned to Caipirasuchus on the basis of a newly discovered specimen referrable to it. MPMA 68-0003/12 consists of a nearly complete cranium and mandible, and a posterior portion of the post-cranium. It was discovered in the municipality of Catanduva, northern São Paulo, from the Adamantina Formation. At least five synapomorphies unite the species, and a phylogenetic analysis found them to be sister taxa.
Caipirasuchus