Synapses are specialized junctions through which neurons signal to each other and to other target cells such as muscles and are crucial to the functioning of the nervous system. However, the mechanism of how the synapses form during development remains poorly understood. In this study, we applied live imaging of fluorescent fusion proteins expressed in the target cells to visualize the process of synapse formation in developing embryos, and showed that a cell adhesion molecule, called Fasciclin2, mediates the cellular interaction between a neuron and its target, that is required for the accumulation of synaptic components. Our results elucidate a molecular mechanism of synapse formation that occurs in an intact organism.