In the auditory cued fear conditioning, memories are stored in synapses between engram neurons, which increased activity during the memory formation. Although molecular imaging of memory-related synapses contributes to deciphering the molecular basis of memory, there is no established method for visualizing them. In this study, we developed a method to selectively visualize synapses between engram neurons, using the c-fos promoter-driven Tet-On system. Tag-fused synaptophysin (tagSyp) and FingR.PSD95 were expressed in presynaptic auditory cortex neurons and postsynaptic lateral amygdala neurons, respectively, in an activity-dependent manner. We found that the number of synapses positive for both tagSyp and FingR.PSD95 in the lateral amygdala was 15-fold higher in mice with cued fear conditioning than in control mice. Thus, we concluded that synapses both positive for tagSyp and FingR.PSD95 correspond to memory-related synapses. Furthermore, combining this method with immunohistochemistry, we found greater amounts of several kinds of synaptic molecules accumulate in memory-related synapses compared to other　synapses. It is expected that our method enables comprehensive analysis of molecular changes in synapses induced by fear memory formation.