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However, morphology\u2010based 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 <jats:italic>Crocodylus<\/jats:italic> species and the subfossil Malagasy genus <jats:italic>Voay<\/jats:italic>, and a distinction between the <jats:italic>Tomistoma<\/jats:italic> and <jats:italic>Gavialis<\/jats:italic> lineages. Our approach is independent of molecular methods but concurs with the molecular topologies. 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