It includes the genera Paralligator, Brillanceausuchus, Kansajsuchus, Shamosuchus, Scolomastax, Sabresuchus, Rugosuchus, Batrachomimus and Wannchampsus, as well as the yet-unnamed "Glen Rose form".

[1][2] Phylogenetic analyses of crocodyliforms find Paralligatoridae to nest within Neosuchia, a large clade (evolutionary grouping) that also includes modern crocodylians.

In crocodyliform phylogeny, paralligatorids are usually found near the base of Neosuchia, outside the clade Eusuchia, which includes crocodylians and their closest relatives.

Below is a cladogram from Montefeltro et al. (2013) showing the phylogenetic relationships of Paralligatoridae:[1] Thalattosuchia Notosuchia Khoratosuchus jintasakuli Tethysuchia Theriosuchus Goniopholididae Bernissartia fagesii Batrachomimus pastosbonensis Shamosuchus spp.

Rugosuchus nonganensis Susisuchus anatoceps Hylaeochampsa vectiana Allodaposuchus precedens Pietraroiasuchus ormezzanoi Iharkutosuchus makadii Isisfordia duncani Crocodylia