The acquisition of a long and slender snout (longirostry) resulted in extreme similar morphology across crocodylians and, therefore, raised a conflict between morphological and molecular phylogenetic hypotheses involving the longirostrine living gharials, Gavialis gangeticus and Tomistoma schlegelii. This discrepancy is not only topological but also concerns divergence time estimates for the crown clade Gavialidae, especially due to the inclusion of another longirostrine forms, ancient ‘thoracosaurs’—which introduces significant chronostratigraphic inconsistencies. To contribute to reconcile these contrasting lines of evidence, exceptionally preserved fossils of a new Miocene gavialid from Peru were included in a total-evidence Bayesian analysis. Our analysis integrates morphological, molecular, and chronostratigraphic data and incorporates most taxa of the largest adaptive radiation of gavialids, which occurred in the Cenozoic of South American and Caribbean (SAC). Our results demonstrate that including SAC taxa substantially increase divergence estimates for Gavialidae, surpassing those inferred from molecular data alone. The exceptional preservation of the new Peruvian fossils enabled character re-evaluation for gavialids and ‘thoracosaurs,’ the latter recovered even outside Crocodylia, and suggesting that longirostry resulted from independent evolution. These findings underscore the crucial role of SAC gavialids for understanding the morphological trajectory and phylogenetics of longirostrine crocodylians.