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Abstract The bony labyrinth of the petrosal bone, a distinctive feature of mammal skulls, is often identified in micro‐computed tomography imaging to infer species' physiological and ecological traits. When done as part of a comparative study, one individual specimen is normally considered representative of a species, and intraspecific variation is considered low. Yet tests of intraspecific variability have been performed on few species and on limited morphological traits. Studies of intraspecific variability are not only valuable to help us assess the need for multiple specimens in comparative work, but relative levels of variability can also be used to reveal insights into a trait's functional significance. In this study, we report measurements of intraspecific variation on two cetaceans with vastly different auditory specializations, a low‐frequency specialized mysticete and an echolocating odontocete. We examine the internal structures of the cochlea in beluga and bowhead whales and relate this to their hearing abilities. Overall levels of intraspecific variability are higher in the bowhead than the beluga, reflecting the more specialized auditory system of the latter. However, the levels of variation differ through the length of the cochlea (base to apex) and these appear to reflect known frequency specializations of the species, with the bowhead having lower variation in some measurements at the low‐frequency apical end than the beluga.