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On the basis of a new, three-dimensionally preserved specimen of the Early Jurassic pterosaur Dorygnathus banthensis we present a reinterpretation of the pterosaur palate. The hard palate is formed by the extensive palatal plate of the maxilla and not by the palatine as has been generally reconstructed. This palatal plate of the maxilla emarginates the choana rostrally and rostrolaterally as in other archosaurs and lepidosaurs. The longitudinally elongate and dorsoventrally flat palatine in Dorygnathus is an isolated bone caudal to the palatal plate of the maxilla and morphologically and topographically it resembles that of crocodilians and birds, respectively. The palatine separates the choana laterally from the suborbital fenestra demonstrating the homologous nature of the (primary) choana in all archosaurs and lepidosaurs. Our study indicates that in basal pterosaurs the pterygo-ectopterygoid fenestra existed caudal to the suborbital fenestra, which became confluent with the adductor chamber in pterodactyloids thereby increasing the relative size of the adductor chamber and hence the mass of the jaw adductors. The choana in basal pterosaurs was relatively small compared with the interpterygoid vacuity. With increasing rostroventral inclination of the quadrates in more derived pterosaurs, the interpterygoid vacuity was reduced considerably, whereas the choana increased in size. This exceptional Dorygnathus specimen also shows a hitherto unknown pair of fenestrae situated at the palatal contact of the premaxilla-maxilla and might represent the aperture for the vomeronasal organ.