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The relative size and shape of the inner ear complex offers proxies for inferring sensory and behavioural characteristics, e.g. visual acuity and locomotory agility. Changes in endosseous labyrinth morphology over time can also be used to trace evolutionary patterns in extinct taxa, such as pterosaurs. Synchrotron X-ray microtomography data of two anhanguerid pterosaur crania from the Araripe Basin (Lower Cretaceous, Northeastern Brazil); the holotype of Tropeognathus mesembrinus and a specimen representing Anhanguera sp., were used here to extract digital endocasts of their endosseous labyrinths. Visual comparison revealed that the inner ear morphologies of the two taxa are remarkably similar. The semicircular canals of Anhanguera sp. are marginally slenderer, especially in the region of the common crus, and more rounded than those of Tropeognathus mesembrinus. Furthermore, this research confirms that the inner ear morphology of Anhanguera sp. is virtually identical to that of Anhanguera santanae (AMNH FARB 25555). Relative to earlier pterosaurs, such as Rhamphorhynchus muensteri and Allkaruen koi, anhanguerids document an evolutionary shift towards proportionally taller anterior semicircular canals, in absence of well-sampled intermediate taxa. The inner ears of the two anhanguerid pterosaurs are relatively large and positioned close to one another, compared to other archosaurs. They also encircle proportionally large floccular lobes, suggesting that anhanguerids had a high degree of visual acuity, which was likely a sensory adaptation for their presumed piscivorous lifestyle.