古神翼龙科与其他翼龙类的关系,以及在神龙翼龙超科的演化位置,长期以来处在争论中,已有许多研究提出不同的演化树。古神翼龙科的成员也有争议,某些研究人员主张掠海翼龙亚科属于古神翼龙科,[3]而其他研究人员认为掠海翼龙亚科较接近新神龙翼龙类的神龙翼龙科。[6]某些研究指出,古神翼龙科可能是个并系群,并非天然生物群,部分物种演化成新神龙翼龙类。[6]以下两个演化树是由David M. Martill、Martill与德恩·奈许(Darren Naish)在2006年提出,第一个是单系群版本,第二个是并系群版本。
^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.