The maxilla was discovered around 1845 during the course of a well excavation in Spring Brook in the New London area and its significance was recognized by geologists John William Dawson and Joseph Leidy.

Dawson brought it to the attention of American paleontologist Joseph Leidy, who described it to the Philadelphia Academy of Natural Sciences in 1854.

[6] Leidy compared Bathygnathus with Thecodontosaurus from the Triassic red beds of the United Kingdom, one of the first dinosaurs to have been described scientifically.

[6] Local naturalist Francis Bain popularized the image of Bathygnathus as a dinosaur in the late 1800s, describing it as a "deep jawed monster" that could attack prey "with a bound of sixteen or eighteen feet... bearing it to the ground with its great weight, while the powerful claws prevented its escape, and the sabre-armed jaws completed the sanguinary work of destruction.

"[2] American paleontologist E. C. Case reclassified Bathygnathus as a pelycosaur (a type of "mammal-like reptile") in 1905, noting its similarities with the genus Dimetrodon, a sail-backed synapsid that was discovered in Texas in the 1870s.