In phylogenetic taxonomy, the clade Pterosauria has usually been defined as node-based and anchored to several extensively studied taxa as well as those thought to be primitive.
One 2003 study defined Pterosauria as "The most recent common ancestor of the Anurognathidae, Preondactylus and Quetzalcoatlus and all their descendants."
However, these types of definition would inevitably leave any related species that are slightly more primitive out of the Pterosauria.
To remedy this, a new definition was proposed that would anchor the name not to any particular species but to an anatomical feature, the presence of an enlarged fourth finger that supports a wing membrane.
A broader clade, Pterosauromorpha, has been defined as all ornithodirans more closely related to pterosaurs than to dinosaurs.

The internal classification of pterosaurs has historically been difficult, because there were many gaps in the fossil record.
Starting from the 21st century, new discoveries are now filling in these gaps and giving a better picture of the evolution of pterosaurs.
Traditionally, they were organized into two suborders: the Rhamphorhynchoidea, a "primitive" group of long-tailed pterosaurs, and the Pterodactyloidea, "advanced" pterosaurs with short tails.
However, this traditional division has been largely abandoned.
Rhamphorhynchoidea is a paraphyletic (unnatural) group, since the pterodactyloids evolved directly from them and not from a common ancestor, so, with the increasing use of cladistics, it has fallen out of favor among most scientists.

The precise relationships between pterosaurs is still unsettled.
Many studies of pterosaur relationships in the past have included limited data and were highly contradictory.
However, newer studies using larger data sets are beginning to make things clearer.
The cladogram (family tree) below follows a phylogenetic analysis presented by Longrich, Martill and Andres in 2018.
In phylogenetic taxonomy, the clade Pterosauria has usually been defined as node-based and anchored to several extensively studied taxa as well as those thought to be primitive. One 2003 study defined Pterosauria as "The most recent common ancestor of the Anurognathidae, Preondactylus and Quetzalcoatlus and all their descendants." However, these types of definition would inevitably leave any related species that are slightly more primitive out of the Pterosauria. To remedy this, a new definition was proposed that would anchor the name not to any particular species but to an anatomical feature, the presence of an enlarged fourth finger that supports a wing membrane. A broader clade, Pterosauromorpha, has been defined as all ornithodirans more closely related to pterosaurs than to dinosaurs.
The internal classification of pterosaurs has historically been difficult, because there were many gaps in the fossil record. Starting from the 21st century, new discoveries are now filling in these gaps and giving a better picture of the evolution of pterosaurs. Traditionally, they were organized into two suborders: the Rhamphorhynchoidea, a "primitive" group of long-tailed pterosaurs, and the Pterodactyloidea, "advanced" pterosaurs with short tails. However, this traditional division has been largely abandoned. Rhamphorhynchoidea is a paraphyletic (unnatural) group, since the pterodactyloids evolved directly from them and not from a common ancestor, so, with the increasing use of cladistics, it has fallen out of favor among most scientists.
The precise relationships between pterosaurs is still unsettled. Many studies of pterosaur relationships in the past have included limited data and were highly contradictory. However, newer studies using larger data sets are beginning to make things clearer. The cladogram (family tree) below follows a phylogenetic analysis presented by Longrich, Martill and Andres in 2018.
Pterosaur