A phylogenetic analysis of dyrosaurids by Hastings et al. (2010) placed Cerrejonisuchus relatively basally in the dyrosaur clade between Phosphatosaurus gavialoides and Arambourgisuchus khouribgaensis.
Below is the cladogram from Hastings et al. (2010) showing the phylogenetic relationship of Cerrejonisuchus within Dyrosauridae:[REF] .