The name derives from the Greek words pteron (πτερόn, meaning 'wing') and daktylos (δάκτυλος, meaning 'finger') and refers to the way in which the wing is supported by one large finger.
Pterodactylus was a relatively small pterosaur genus, with adult wingspans ranging from 50 centimeters (1.5 ft) in P. kochi to 2.4 (8 ft) meters in P. grandis. Other species were smaller, with some such as P. micronyx representing especially tiny individuals. However, these smaller "species" probably represent juvenile specimens of Pterodactylus, Germanodactylus, and/or Gnathosaurus.
In 1998, the discovery of one specimen assigned to P kochi shed light on the life appearance of Pterodactylus, as it preserved unique soft-tissue traits not present in previous fossil skeletons. Like other ctenochasmatoids, Pterodactylus was found to have a striated soft-tissue crest on the skull. Soft tissue impressions also showed unusually long, sharp, and recurved keratin sheaths on its claws. It was covered in hair-like integument, with a mane of longer hair running down the back of its neck. The feet also showed evidence of webbing.
The animal now known as Pterodactylus was the first pterosaur ever to be identified. The first Pterodactylus specimen was described by the Italian scientist Cosimo Collini in 1784, based on a fossil skeleton unearthed from the Solnhofen limestone of Bavaria. Collini was the curator of the "Naturalienkabinett", or nature cabinet (a precursor to the modern concept of the natural history museum), in the palace of Charles Theodore, Elector of Bavaria. Collini, however, did not recognize the specimen as a flying animal. In fact, Collini could not fathom what kind of animal it might have been. He speculated that it may have been a sea creature, not for any anatomical reason, but because he thought the ocean depths were more likely to have housed unknown types of animals. The idea that pterosaurs were aquatic animals persisted among a minority of scientists as late as 1830, when the German zoologist Johann Georg Wagler published a text on "amphibians" which included an illustration of Pterodactylus using its wings as flippers. Wagler went so far as to classify Pterodactylus, along with other aquatic vertebrates (namely plesiosaurs, ichthyosaurs, and monotremes), in the class Gryphi, between birds and mammals. It was the German scientist Johann Hermann who first recognized that Pterodactylus used its long fourth finger to support a wing membrane. In 1800, Hermann alerted the French scientist George Cuvier to the existence of the fossil, believing that it would be captured by the occupying armies of Napoleon and sent to France (and likely to Cuvier himself) for study. Hermann sent Cuvier a letter containing his own interpretation of the specimen (though he had not examined it personally), which he believed to be a mammal, including the first known life restoration of a pterosaur. Hermann restored the animal with wing membranes extending from the long fourth finger to the ankle and a covering of fur (neither wing membranes nor fur had been preserved in the specimen). Hermann also added a membrane between the neck and wrist, as is the condition in bats. Cuvier agreed, and at Hermann's suggestion became was the first to publish these ideas in December 1800. Cuvier remarked, "[It is not possible to doubt that the long finger served to support a membrane that, by lengthening the anterior extremity of this animal, formed a good wing.]"
It was not until 1817 that a second specimen of Pterodactylus came to light, again from Solnhofen. This tiny specimen was described by Soemmerring as Ornithocephalus brevirostrus (for its short snout, now understood to be a juvenile character), and provided a restoration of the skeleton, the first one published for any pterosaur.
Hermann von Meyer, in 1830, named the family Pterodactylidae to contain Pterodactylus and other pterosaurs known at the time. This family has more recently been used to refer to many similar species from Germany and elsewhere, though recent studies suggest it may be a paraphyletic or polyphyletic unnatural grouping with respect to more advanced members of the Ctenochasmatoidea (or Archaeopterodactyloidea).
Many species assigned to Pterodactylus have been based on juvenile specimens, and have subsequently been recognized as immature individuals of other species or genera. P. elegans, for example, was found by numerous studies to be an immature Ctenochasma. Another species of Pterodactylus based on small, immature specimens is P. micronyx. However, it has been difficult to determine exactly of what genus and species P. micronyx might be the juvenile form. Christopher Bennett and others have suggested it may belong to Gnathosaurus subultus.
During its over 200 year history, the various species of Pterodactylus have gone through a number of changes in classification, and thus have acquired a large number of synonyms. Additionally, a number of species assigned to Pterodactylus are based on poor remains that have proven difficult to assign to one species or another, and are therefore considered nomena dubia ("doubtful names").