古神翼龍科與其他翼龍類的關係，以及在神龍翼龍超科的演化位置，長期以來處在爭論中，已有許多研究提出不同的演化樹。古神翼龍科的成員也有爭議，某些研究人員主張掠海翼龍亞科屬於古神翼龍科，[3]而其他研究人員認為掠海翼龍亞科較接近新神龍翼龍類的神龍翼龍科。[6]某些研究指出，古神翼龍科可能是個並系群，並非天然生物群，部份物種演化成新神龍翼龍類。[6]以下兩個演化樹是由David M. Martill、Martill與德恩·奈許（Darren Naish）在2006年提出，第一個是單系群版本，第二個是並系群版本。
^Lü, J., Jin, X., Unwin, D.M., Zhao, L., Azuma, Y., and Ji, Q. (2006). A new species of Huaxiapterus (Pterosauria: Pterodactyloidea) from the Lower Cretaceous of western Liaoning, China with comments on the systematics of tapejarid pterosaurs. Acta Geologica Sinica80(3):315-326.
^ 3.03.13.2Kellner, A.W.A.; and Campos, D.A. Short note on the ingroup relationships of the Tapejaridae (Pterosauria, Pterodactyloidea. Boletim do Museu Nacional. 2007, 75: 1–14.引文使用过时参数coauthors (帮助)
^Lü, J., Unwin, D.M., Xu, L., and Zhang, X. (2008). "A new azhdarchoid pterosaur from the Lower Cretaceous of China and its implications for pterosaur phylogeny and evolution." Naturwissenschaften,
^Martill, D.M., Bechly, G., and Heads, S.W. (2007). "Appendix: species list for the Crato Formation." In: Martill, D.M., Bechly, G., and Loveridge, R.F. (eds.), 2007. The Crato Fossil Beds of Brazil: Window into an Ancient World. Cambridge University Press, Cambridge. Pp. 582–607.
^ 6.06.1Martill, D.M. and Naish, D. (2006). "Cranial crest development in the azhdarchoid pterosaur Tupuxuara, with a review of the genus and tapejarid monophyly." Palaeontology, 49: 925-941.
