In mossy fiber synapses of the CA3 region of the hippocampus, long-term potentiation (LTP) is induced presynaptically by activation of cAMP-dependent protein kinase A (PKA). Rab3A is a synaptic vesicle protein that regulates vesicle fusion and is essential for mossy fiber LTP. Rab3A probably acts via two effector proteins, rabphilin and RIM, of which rabphilin is an in vitro substrate for PKA. To test if rabphilin is phosphorylated in nerve terminals and if its PKA-dependent phosphorylation correlates with the PKA-dependent induction of LTP in mossy fiber terminals, we have studied the phosphorylation of rabphilin in synaptosomes isolated from the CA1 and CA3 regions of the hippocampus. Rabphilin was phosphorylated in both CA1 and CA3 synaptosomes. However, when we treated the CA1 and CA3 synaptosomes with forskolin (an agent that enhances PKA activity) or induced Ca2+ influx into synaptosomes with high K+, rabphilin phosphorylation was increased selectively in mossy fiber CA3 synaptosomes, but not in CA1 synaptosomes. In contrast, the phosphorylation of synapsin, studied as a control for the specificity of the region-specific phosphorylation of rabphilin, was augmented similarly by both treatments in CA1 and CA3 synaptosomes. These results reveal that the phosphorylation states of two synaptic substrates for PKA and CaM KII, rabphilin and synapsin, are regulated differentially in a region-specific manner, an unexpected finding because rabphilin and synapsin are similarly present in CA1 and CA3 synaptosomes and are colocalized on the same synaptic vesicles. The region-specific phosphorylation of rabphilin agrees well with the restricted induction of LTP by presynaptic PKA activation in mossy fiber, but not CA1, nerve terminals.