Pterodactylidae is a controversial group of pterosaurs. During the 2000s and 2010s, several competing definitions for the various Jurassic pterodactyloid groups were proposed. Pereda-Suberbiola et al. (2012) used Fabien Knoll's (2000) definition of the name Pterodactylidae. Knoll had defined Pterodactylidae as a clade containing "Pterodactylus antiquus, Ctenochasma elegans, their most recent common ancestor and all its descendants". Using this definition with the analysis conducted by Pereda-Suberbiola et al. (2012) meant that Ctenochasmatoidea was nested inside Pterodactylidae.

Classification

Below is the majority-rule consensus tree found by Pereda-Suberbiola et al. (2012), showing their preferred definitions of Pterodactylidae and Ctenochasmatoidea. Other researchers, such as David Unwin, have traditionally defined Pterodactylidae in such a way to ensure it is nested within Ctenochasmatoidea instead. In 2003, Unwin defined the same clade (Pterodactylus + Pterodaustro) with the name Euctenochasmatia. Unwin considered this to be a subgroup within Ctenochasmatoidea, but most analyses since have found Pterodactylus to be more primitive than he thought, making Euctenochasmatia the more inclusive group.