Presynaptic varicosities of central GABAergic neurons contain GABA release machinery and cell adhesion molecules, whereas postsynaptic sites of dendritic shafts are endowed with clusters of GABA receptors, scaffolding proteins and cell adhesion molecules. Presynaptic cell adhesion protein, neurexin-1β (NXN-1β), and postsynaptic neuroligin-2 (NL-2) are implicated in inhibitory synapse development, however, their precise roles have to be unraveled. Using primary culture of mouse hippocampal neurons derived from VGAT-Venus mice (Wang et al., 2009) and triple wavelength confocal microscopy, this study therefore aimed at examining morphology and localization changes of three synaptic elements that included presynaptic varicosities, postsynaptic scaffolding protein, gephyrin, and cell adhesion proteins, NXN-1β or NL-2. GABAergic inhibitory neurons extended their axons to dendritic sites of pyramidal neuron and formed axon-dendritic contacts where gephyrin clusters overlapped. These contact sites between presynaptic axonal varicosities and postsynaptic gephyrin clusters could be inhibitory GABAergic synapses. The majority of such contact sites contained NXN-1β and NL-2 clusters even in early culture phase. NXN-1β clusters were localized in axonal varicosities, while NL-2 clusters were colocalized with postsynaptic gephyrin clusters in dendritic shafts. Time-lapse imaging revealed that NXN-1β and NL-2 clusters actively moved within the synaptic contact sites and ceaselessly changed their fluorescent intensity, whereas gephyrin clusters stayed relatively stably. The results demonstrate that neurexin/neuroligin-2 are localized in synaptic contact sites at an early stage of inhibitory synapse development and suggest that active movements of the neurexin/neuroligin-2 complex could regulate the strength of GABAergic inhibitory synaptic connections.