After recognising the fundamentally different snout shape, Wagner, after previous failed attempts by Leopold Fitzinger and Christoph Gottfried Andreas Giebel, who used preoccupied names, in 1861 named a distinct genus: Scaphognathus, derived from Greek skaphe, "boat" or "tub", and gnathos, "jaw", in reference to the blunt shape of the lower jaws.

[3] In the early twentieth century, the "rhamphorhynchoid" nature of S. crassirostris was recognized after the discovery of the second specimen in Mühlheim, whose long tail was preserved.

The second Scaphognathus specimen was more complete than its predecessor, but only half the size (twenty inch wingspan) and with partially ossified bones.

[6] The cladogram (family tree) of rhamphorhynchids below is the result of a large phylogenetic analysis published by Andres & Myers in 2013.

[7] Scaphognathus crassirostris Dorygnathus banthensis Cacibupteryx caribensis Nesodactylus hesperius Rhamphorhynchus muensteri Harpactognathus gentryii Angustinaripterus longicephalus Sericipterus wucaiwanensis