Memories are thought to be stored as plastic changes in synapses between neurons activated during memory formation. Although molecular imaging of such memory-related synapses would contribute 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 neurons that are activated during memory formation 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 tagSyp/FingR.PSD95 double positive synapses correspond to memory-related synapses. We also demonstrate that our method is compatible with immunohistochemistry and nanometer-resolution molecular imaging, including STORM, enabling quantification of endogenous synaptic proteins specifically at memory-related synapses. It is expected that our method will open the way for comprehensive analysis of molecular changes in synapses induced by memory formation.