The precise assembly of inner ear hair cell stereocilia into rows of increasing height is critical for mechanotransduction and the sense of hearing. Yet, how the lengths of actin-based stereocilia are regulated remains poorly understood. Mutations of the molecular motor myosin-15 stunt stereocilia growth and cause deafness. We found that hair cells express two isoforms of myosin-15 through alternative splicing of an N-terminal domain, and that these isoforms selectively traffic to different stereocilia rows. Using an isoform-specific knockout mouse, hair cells expressing only the small isoform remarkably develop normal stereocilia bundles. However, a critical subset of stereocilia with active mechanotransducer channels subsequently retracts. The larger isoform with the N-terminal domain traffics to these specialized stereocilia and prevents disassembly of their actin core. Our results show that myosin-15 isoforms can navigate between functionally distinct classes of stereocilia, and are independently required to assemble and then maintain the intricate hair bundle architecture.