At present Scaphognathus is known from three specimens, all of which originated in the Kimmeridgian-age Solnhofen Limestone. Physically it was very similar to Rhamphorhynchus, albeit with notable cranial differences.
For one, Scaphognathus had a proportionately shorter skull (4.5 in) with a blunter tip and a larger antorbital fenestra. Its teeth oriented vertically rather than horizontally. The traditional count of them held that eighteen teeth were in the upper jaws and ten in the lower. S. Christopher Bennett, studying a new third specimen, SMNS 59395, in 2004 determined there were only sixteen teeth in the upper jaws, the higher previous number having been caused by incorrectly adding replacement teeth.
Comparisons between the scleral rings of Scaphognathus and modern birds and reptiles suggest that it may have been diurnal. This may also indicate niche partitioning with contemporary pterosaurs inferred to be nocturnal, such as Ctenochasma and Rhamphorhynchus.
Scaphognathus can be created in Jurassic World: The Game as a legendary pterosaur.