Cochlear neurons innervate the brainstem cochlear nucleus in a tonotopic fashion according to their sensitivity to different sound frequencies (known as the neuron’s characteristic frequency). It is unclear whether these neurons with distinct characteristic frequencies use different strategies to innervate the cochlear nucleus. Here, we use genetic approaches to differentially label spiral ganglion neurons (SGNs) and their auditory nerve fibers (ANFs) that relay different characteristic frequencies in mice. We found that SGN populations that supply distinct regions of the cochlea employ different cellular strategies to target and innervate neurons in the cochlear nucleus during tonotopic map formation. ANFs that will exhibit high-characteristic frequencies initially overshoot and sample a large area of targets before refining their connections to correct targets, while fibers that will exhibit low-characteristic frequencies are more accurate in initial targeting and undergo minimal target sampling. Moreover, similar to their peripheral projections, the central projections of ANFs show a gradient of development along the tonotopic axis, with outgrowth and branching of prospective high-frequency ANFs initiated about two days earlier than those of prospective low-frequency ANFs. The processes of synaptogenesis are similar between high- and low-frequency ANFs, but a higher proportion of low-frequency ANFs form smaller endbulb synaptic endings. These observations reveal the diversity of cellular mechanisms that auditory neurons that will become functionally distinct use to innervate their targets during tonotopic map formation.