[1] Knoll had defined Pterodactylidae as a clade containing "Pterodactylus antiquus, Ctenochasma elegans, their most recent common ancestor and all its descendants".

[2] Using this definition with the analysis conducted by Pereda-Suberbiola et al. (2012) meant that Ctenochasmatoidea was nested inside Pterodactylidae.

[1] Below is the majority-rule consensus tree found by Pereda-Suberbiola et al. (2012), showing their preferred definitions of Pterodactylidae and Ctenochasmatoidea.

[1] Pterodactylus Prejanopterus Cycnorhamphus Cearadactylus Gnathosaurus Pterodactylus longicolum Pterodaustro Ctenochasma Gegepterus Eosipterus Other researchers, such as David Unwin, have traditionally defined Pterodactylidae in such a way to ensure it is nested within Ctenochasmatoidea instead.

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.