Choristoderes are extinct semi-aquatic to aquatic diapsid reptiles, occupying a similar niche as modern crocodilians from the Jurassic to the Miocene. Distinct from other diapsids, choristoderes have a neomorphic ossification between the braincase, squamosal, and quadrate. This neomorphic bone is described as thin and plate-like in long-snouted choristoderes (Neochoristodera), yet little is known about its presence and morphology in short-snouted non-neochoristoderes that are sister groups to Neochoristodera. Using X-ray micro-CT scanning, this study describes in detail the neomorph of two non-neochoristoderes, Coeruleodraco jurassicus and Philydrosaurus proseilus. The neomorph of both species is found between the parietal, quadrate, and squamosal. The shape of the neomorph resembles a pyramid in three-dimensions, with a triangular dorsal surface and a prominent ventral process. This confirms the neomorph is shared among early and late branching choristoderes; therefore, presence of the neomorph is a potential synapomorphy of Choristodera. In addition, the pterygoquadrate foramen is identified in non-neochoristoderes for the first time, located between the neomorph and quadrate in C. jurassicus. In the holotype of P. proseilus, the neomorph and quadrate were dislocated, but a possible pterygoquadrate foramen is identified between the two bones. Although the neomorph and pterygoquadrate foramen have been suggested to be homologous with the stapes and stapedial foramen in Champsosaurus, more evidences are required to confirm this homology in non-neochoristoderes, because 1) the neomorph is long and plate-like in neochoristoderes, but pyramid-shaped in non-neochoristoderes; 2) in Champsosaurus, the neomorph is situated lateral to the prootic and opisthotic; in C. jurassicus and P. proseilus, articulation between the neomorph and prootic (or opisthotic) cannot be confirmed due to damage to the braincase during preservation. To understand the origin of the neomorph, more intact specimens are needed to assess contact relationships between the neomorph and otic region in non-neochoristoderes.