Characterizing the phenotype of wild versus domesticated forms is a fundamental step to understand how the domestication process has affected morphospace occupation. In the case of dogs the extent of divergence in different organs is a rich subject when considering the diversity of breeds. We present a comprehensive morphometric study of the osseous inner ear, considered a highly conserved structure in mammals. It houses the sense of balance in the vestibular organ, including the semicircular canals, and the cochlea, associated with the perception of sound waves. Three dimensional virtual endocasts obtained from high-resolution computed tomography scans were used to characterize the inner ear of 35 dogs of three ‘ancient’ (‘basal’) and 13 ‘modern’ breeds, 13 wolves, and six dingoes, which are feral dogs, using semilandmarks. In comparison to wolves, ‘modern’ dog breeds exhibit larger variationin the morphology of the inner ear. The structures of the inner ear of ‘ancient’ dog breeds also occupy a morphospace outside the range of the wolves. The number of turns of the cochlea is uniform in wolves whereas the range is extended in dogs. The domestication process and the selection of breeds have produced shapesoutside the normal range of variation of the species, illustrating the plasticity of development of conserved structures. Zooarcheological studies could incorporate the study of petrosal bones in the identification of domesticated dogs.