We review the molecular basis of the auditory system development and evolution. The auditory periphery evolved by building on the capacity of vestibular hair cells to respond to higher frequency mechanical stimulation. Evolution altered accessory structures to transform vestibular to auditory receptors. Auditory neurons are derived from vestibular neurons, possibly through the expression of the zinc finger protein GATA3. The bHLH gene Neurogenin1 is expressed in the area of the developing vestibular nuclei whereas the bHLH gene Atoh1 is expressed in the developing auditory nuclei. Atoh1 null mice show an almost complete loss of cochlear nuclei. Overall, the ear, sensory neurons and brainstem auditory nuclei show molecular conservation embedded in an organ-specific molecular context. This results in the modification of the developmental pathways governed by these conserved molecules. These data are consistent with the emerging insight that morphological evolution is primarily driven by the modification of gene expression regulation.