Tonotopic organization is a fundamental feature of the auditory system. In the developing auditory brainstem, the ontogeny and maturation of neurotransmission progress from high to low frequencies along the tonotopic axis. To explore the underlying mechanism of this tonotopic development, we aim to determine whether the presynaptic machinery responsible for neurotransmitter release is tonotopically differentiated during development. In the current study, we examined vesicular neurotransmitter transporters and calcium sensors, two central players responsible for loading neurotransmitter into synaptic vesicles and for triggering neurotransmitter release in a calcium-dependent manner, respectively. Using immunocytochemistry, we characterized the distribution patterns of vesicular glutamate transporters (VGLUTs) 1 and 2, vesicular gamma-aminobutyric acid transporter (VGAT), and calcium sensor synaptotagmin (Syt) 1 and 2 in the developing mouse medial nucleus of the trapezoid body (MNTB). We identified tonotopic gradients of VGLUT1, VGAT, Syt1, and Syt2 in the first postnatal week, with higher protein densities in the more medial (highfrequency) portion of the MNTB. These gradients gradually flattened before the onset of hearing. In contrast, VGLUT2 was distributed relatively uniformly along the tonotopic axis during this prehearing period. In mice lacking Fragile X mental retardation protein, an mRNA-binding protein that regulates synaptic development and plasticity, progress to achieve the mature-like organization was altered for VGLUT1, Syt1, and Syt2, but not for VGAT. Together, our results identified novel organization patterns of selective presynaptic proteins in immature auditory synapses, providing a potential mechanism that may contribute to tonotopic differentiation of neurotransmission during normal and abnormal development.