Narwhals (Monodon monoceros) and belugas (Delphinapterus leucas) are the only extant members of the Monodontidae, and are charismatic Arctic‐endemic cetaceans that are at risk from global change. Investigating the anatomy and sensory apparatuses of these animals is essential to understanding their ecology and evolution, and informs efforts for their conservation. Here, we use X‐ray CT scans to compare aspects of the endocranial and inner ear labyrinth anatomy of extant monodontids and use the overall morphology to draw larger inferences about the relationship between morphology and ecology. We show that differences in the shape of the brain, vasculature, and neural canals of both species may relate to differences in diving and other behaviors. The cochleae are similar in morphology in the two species, signifying similar hearing ranges and a close evolutionary relationship. Lastly, we compare two different methods for calculating 90var – a calculation independent of body size that is increasingly being used as a proxy for habitat preference. We show that a ‘direct’ angular measurement method shows significant differences between Arctic and other habitat preferences, but angle measurements based on planes through the semicircular canals do not, emphasizing the need for more detailed study and standardization of this measurement. This work represents the first comparative internal anatomical study of the endocranium and inner ear labyrinths of this small clade of toothed whales.