In a temperature-sensitive Drosophila mutant, shibire, synaptic vesicles are completely depleted in nerve terminals after stimulation at 34°C, but upon returning to 22°C, endocytosis resumes. In this study, synaptic vesicles in the boutons of nerve terminals at the mutant neuromuscular junction were loaded with a fluorescent dye, FM1-43, during vesicle reformation at 22°C after complete depletion at 34°C. We found two distinct pools of synaptic vesicles, namely an exo/endo cycling pool, located in the periphery of the bouton, and a reserve pool, located in its center. Cytochalasin D treatment eliminated the reserve pool and reduced synaptic transmission evoked by high frequency stimulation. Thus, the reserve pool may play a crucial role for sustaining high frequency synaptic transmission.