SummaryAll synapses require fusion-competent vesicles and coordinated Ca2+-secretion coupling for neurotransmission, yet functional and anatomical properties show a high diversity across different synapse types. We show here that the presynaptic protein RIM-BP2 has diversified functions in neurotransmitter release at different central mammalian synapses and thus contributes to synaptic diversity. At hippocampal pyramidal CA3-CA1 synapses, RIM-BP2 loss has a mild effect on neurotransmitter release, by only regulating Ca2+-secretion coupling. However, at hippocampal mossy fiber synapses RIM-BP2 has a strong impact on neurotransmitter release by promoting vesicle docking/priming via recruitment of Munc13-1. In wild type mossy fiber synapses, the distance between RIM-BP2 clusters and Munc13-1 clusters is larger than in hippocampal pyramidal CA3-CA1 synapses, suggesting that spatial organization may dictate the role a protein plays in synaptic transmission and that differences in active zone architecture is a major determinant factor in the functional diversity of synapses.