Bony fishes have a well-developed acoustic and vestibular sense, which is registered in the highly specialized otolithic end-organ containing a pair of three aragonitic otoliths. Usually, the largest otolith is the sagitta, which is considered to be primarily responsible for sound detection and is known to be morphologically diverse and specific across species and higher taxonomic levels. We investigated sagittal otoliths of abyssal and hadal fishes of three families containing taxa adapted to these deep habitats: the Liparidae (snailfishes), Macrouridae (rattails), and Ophidiidae (cusk eels). The purpose of our study was to ascertain whether specific depth-dependent effects on otolith size or morphology could be observed in comparison to the shallower-living counterparts in these groups. We were able to identify a trend toward size reduction in otoliths with depth and certain “simplifications” in otolith morphology. However, we also observed that such trends would only become detectable when studying otoliths within well-defined clades because of the many complexities that occur in otolith morphologies that are unrelated to habitat depth. We propose future work to study freshly caught hadal liparids for the physiology of the otolith end-organ and macula acustica to learn more about the functioning of the organ in fishes living at great depths. Together these findings provide new insights into the drivers of otolith diversity and the evolution of fishes into deep-sea environments.