Rupert classified the new species within Rhamphorhynchidae, of which group very old species are known such as Dorygnathus, but soon it was understood the form was much more basal. A cladistic analysis by David Unwin found Preondactylus as the most basal pterosaur, and the species was accordingly used by him for a node clade definition of the clade Pterosauria. Other analyses however, have found a somewhat more derived position for Preondactylus.