Pholidosauridae is usually considered to be most closely related to the Dyrosauridae. However, the relationship between these families isn't fully understood. Pholidosauridae might be monophyletic,paraphyletic or even a polyphyletic in relation to Dyrosauridae. For example, Fortier, Perea & Schultz (2011) found the family to be monophyletic, and include to main lineages: the Elosuchus–Meridiosaurus lineage and the Pholidosaurus lineage. The cladogram below shows their phylogenetic analysis, which is based on an expanded version of Pol and Gasparini (2009) analysis.
de Andrade et al. (2011) recovered a paraphyletic traditional Pholidosauridae. In their analysis the "Elosuchus lineage" was found to be basal to the "Pholidosaurus lineage"+Dyrosauridae. They used the name Elosuchidae for the Elosuchus lineage and restricted Pholidosauridae to its type genus. The following cladogram simplified after their analysis.