Systematics is the science of arranging organisms into a logical classification of hierarchical structures. Essentially, this is a means of forming family trees of organisms over time.

This is difficult to achieve with organisms like pterosaurs since their overall structure has evolved to optimize flying ability. The difficulty is simply that different families of pterosaurs will eventually evolve similar flight structures because they favour survival and enable more effective mating. This results in very similar species that may not be directly related. This phenomenon is called convergence.

The Order Pterosauria is part of the much larger Phylum, Vertebrata, since all of the pterosaurs have backbones.

Pterosaurs are classified into sub-order based upon the tail and wing metacarpal structure. The two sub-orders are the Rhamphorhynchoidea with long tails and short wing metacarpals and the Pterodactyloidea with short tails and long wing metacarpals.

The families are grouped into types that have overall similar skeletal features and skull structures. This can be a little uncertain where a specimen is only known from a small skeletal fragment. In such cases the classification is made in a tentative way and may be changed if more information suggests otherwise.

Genus groupings are made where there is a certainty that specimens are strongly related by skeletal structures and other factors. Things such as a characteristic crest, as seen in the Germanodactylidae.

Species groupings are based on all skeletal structures between individuals being the same. Key features are related to measurements and assumed knowledge on growth and development of organisms. Since there are no living pterosaurs, the classic test of a species cannot be applied.

Species: "Individuals who can breed and produce viable offspring."

When dealing with fossil organisms, the term "clade" is more appropriate since the breeding test cannot be carried out.  The term clade is applied to any group of organisms that share a wide range of common features.

An example of the classification of a pterosaur is given below;

Kingdom Animalia  
Phylum Vertebrata  
Class Reptilia  
Sub-class Archosauria  
Order Pterosauria  
Sub-Order Pterodactyloidea Plieninger 1901
Family Germanadactylidae Young 1964
Genus Germanodactylus Young 1964
Species cristatus Wiman 1925

The species known by the binomial name of Germanodactlyus cristatus was first described as Pteroidactylus cristatus in 1925 by C. Wiman. The fossil came from the Solnhofen Limestone of Bavaria in Germany. It was later re-named by the Chinese palaeontologist C. C. Young in 1964 when it was found to be different from other pterodactyls, and moved into a family group of its own.