Neurotransmitter release is confined to a specialized area of the presynaptic plasma membrane known as the active zone which consists of a large number of synaptic proteins including Munc13. The composition and in situ arrangement of the active zone proteins remain unclear. In this study, we developed an optimized immunostaining method to visualize active zone proteins at synapses in the hippocampus, and analyzed their nanoscale spatial distribution by multi-color and three-dimensional super-resolution imaging. We found that active zone proteins form discrete nanoscale supramolecular assemblies in an ordered arrangement as we have previously found for Munc13 proteins. The distance of individual supramolecular assemblies to Munc13 assembly, which marks the synaptic vesicle release site, varied among active zone proteins. Interestingly, the composition and distribution of active zone proteins varied among types of synapses, e.g. Schaffer collateral synapses, perforant path synapses, and mossy fiber synapses. Our results provide insight into supramolecular structure responsible for universality and diversity of synaptic functions.