The phylogenetic relationships within crown Crocodylia remain contentious due to conflicts between molecular and morphological hypotheses. However, morphology‐based datasets are mostly constructed on external characters, overlooking internal structures. Here, we use 3D geometric morphometrics to study the shape of the intertympanic sinus system in crown crocodylians during ontogeny, in order to assess its significance in a taxonomic context. Intertympanic sinus shape was found to be highly correlated with size and modulated by cranial shape during development. Still, adult sinus morphology distinguishes specimens at the family, genus and species level. We observe a clear distinction between Alligatoridae and Longirostres, a separation of different Crocodylus species and the subfossil Malagasy genus Voay, and a distinction between the Tomistoma and Gavialis lineages. Our approach is independent of molecular methods but concurs with the molecular topologies. Therefore, sinus characters could add significantly to morphological datasets, offering an alternative viewpoint to resolve problems in crocodylian relationships.
We recognised the usefulness of the paratympanic sinuses in distinguishing major lineages within Crocodylia. 3D geometric morphometric approaches allow us to quantify the ontogeny and variability of the intertympanic sinus within one of the largest dataset of modern species, including one of the largest specimens ever scanned at such a high resolution. We identify internal structures that are clade‐specific and show the potential of those being used in phylogenetic datasets in order to solve major contentions among the Crocodylia, including the long‐standing Tomistoma‐ Gavialis debate.