Bones of Mesosuchus were first found by David Meredith Seares Watson in 1912 after examining a block of sandstone kept in a private collection of Alfred Brown.

[2] This block was found in the middle deposits of the Burgersdorp Formation,[3] in the Cynognathus Assemblage Zone near the town of Aliwal North in the Cape Province of South Africa.

As the etymology of the name suggests, Watson believed that Mesosuchus was an ancestral crocodile with close affinities to other presumed primitive crocodilians such as Proterosuchus, Erythrosuchus, and Ornithosuchus.

Broom designated an articulated skeleton with a single external naris and a pair of supposed acrodont premaxillary teeth as the type of Mesosuchus,[2] and the remainder of the specimens were assigned to a new genus and species, Euparkeria capensis.

SAM 5882, the holotype for Mesosuchus, consists of a partial rostrum, palate, braincase, lower jaws, sections of articulated presacral vertebral column, nine articulated caudal vertebrae, portions of scapula and pelvic girdle, and partial forelimb and hindlimbs.

[5] SAM 6536, another paratype, consists of a virtually complete skull with lower jaws, articulated cervical vertebrae and ribs, dorsal vertebrae and ribs, complete left scapulocoracoid and partial right scapula, interclavicle, clavicles, distal end of left humerus, and gastralia.

[5] SAM 7416, another paratype, consists of an articulated vertebral column composed of the last dozen presacrals, both sacrals and at least the first 15 caudal vertebrae, fragments of right forelimb, pelvic girdle, complete right femur, right crus and partial left crus, and right and left tarsi and pedes.

One feature on the skull that can distinguish the Mesosuchus from all other rhynchosaurs, with possible exception of Howesia, is the presence of a beak-like rostrum, formed primarily by huge premaxillary teeth rather than by tapering, edentulous premaxillae.

The posterodorsal process forms a great portion of the smooth cranial rim of the upper temporal fenestra and contacts the parietal below the postfrontal.

When looking at the different parts however, there are indications of at least six elements present in the lower jaw of the Mesosuchus: dentary, splenial, surangular, angular, prearticular, and articular.