The cytoskeletal matrix of the active zone and synaptic voltage-dependent calcium channels (VDCCs) are both necessary components for the organization and regulation of synaptic vesicle release. In this study, we report a novel interaction between the cytoskeletal matrix of the active zone protein, ELKS1b, and the VDCC subunit, β4, in the molecular layer of the cerebellum. We found that the two proteins coimmunoprecipitated using antibodies against each protein. Using fluorescent immunohistochemistry, we observed colocalization between ELKS1b and VDCC β4 in the molecular layer of the cerebellum, suggesting that these proteins are both present in molecular layer synapses. Analysis of a P/Q-type VDCC knockout mouse (Cacna1a(-/-)) revealed that the localization of the VDCC β4 subunit to the molecular layer was disrupted, although ELKS1b protein localization was not affected. These results demonstrate that these two proteins interact in vitro and colocalize in the cerebellum, and suggest that their interaction may play a role at the molecular layer synapses of the cerebellum.