Similarities of acoustic tasks performed by odontocetes and microchiropteran insectivorous bats suggest they have common auditory ultrasonic signal processing mechanisms. However, there are also significant differences among these earsrelated to operating in water vs. air. We compared the anatomy of the peripheral auditory system of two species of FM bat (big brown bat Eptesicus fuscus; Japanese house bat Pipistrellus abramus) and tw odontocetes (harbor porpoise Phocoena phocoena; bottlenose dolphin Tursiops truncatus) using ultra high resolution (11–100 micron) isotropic voxel computed tomography (helical and microCT). Significant differences were found for the stapes-oval window location (the point of input of sound to the inner ear) in these species compared to most mammals. Further, the porpoise’s basilar membrane includes a “foveal” region with “stretched” frequency representation and relatively constant membrane thickness/width ratios similar to those previously reported for some bat species. In the bats, the stapes is located above the hook which may create bi-directional sound energy propagation. In the porpoise, there is a narrow double hook which we hypothesize limits the penetration of low frequency signals into the cochlea. Both bats and porpoises have low ratios of cochlear radii, which also curtails low frequency admission.These specializations result in an inner ear with the majority of the hair cells and neurons devoted to high frequency transduction.