AbstractSynaptic scaffolding molecule (S‐SCAM) is a synaptic protein, which harbors five or six PSD‐95/Discs large/ZO‐1 (PDZ), a guanylate kinase and two WW domains. It interacts with NMDA receptor subunits, neuroligin and β‐catenin, and is involved in the accumulation of neuroligin at excitatory synapses. In this study, we have demonstrated S‐SCAM is localized at inhibitory synapses in rat primary cultured hippocampal neurons. We have identified β‐dystroglycan (β‐DG) as a binding partner for S‐SCAM at inhibitory synapses. WW domains of S‐SCAM bind to three sequences of β‐DG. We have also revealed that S‐SCAM can interact with neuroligin 2, which is known to be exclusively localized at inhibitory synapses. The WW domains and the second PDZ domain of S‐SCAM are involved in the interaction with neuroligin 2. β‐DG, neuroligin 2 and S‐SCAM form a tripartite complex in vitro. Neuroligin 2 is detected in the immunoprecipitates by anti‐β‐DG antibody from rat brain. S‐SCAM, β‐DG and neuroligin 2 are partially co‐localized in rat hippocampal neurons. These data suggest that S‐SCAM is associated with β‐DG and neuroligin 2 at inhibitory synapses, and functions as a linker between the dystrophin glycoprotein complex and the neurexin–neuroligin complex.