Acoustic task similarities of odontocetes (toothed whales) and microchiropterans (insectivorous bats) suggest they have common biosonar mechanisms. However, media differences; e.g., sound speeds in air versus water, may have driven variations in auditory system adaptations. We examined the peripheral auditory system of an FM bat (big brown bat Eptesicus fuscus) and two toothed whale species (harbor porpoise Phocoena phocoena; bottlenose dolphin Tursiops truncatu) using ultra high resolution (11 μm) isotropic voxel microCT. Significant differences were found among species for oval window location, cochlear length, basilar membrane gradients, cochlear spiral morphometry, cochlear curvature, and basilar membrane stiffness. High and low frequency hearing range cut-offs correlate with basilar membrane thickness/width ratios and cochlear radii of curvature. These features predict species specific high and low frequency hearing limits. Harbor porpoises, the highest frequency echolocator in the study, have large basal basilar membrane ratios and a “foveal” region with a constant membrane ratio similar to those reported for some bat species, consistent with a “stretched” frequency region. Furthermore, both the bats and harbor porpoises examined displayed unusual stapedial input locations and tightly coiled cochleae, specializations that may enhance ultrasonic frequency signal resolution and diminish low frequency cochlear propagation.