Superresolution microscopy techniques such as STED, STORM/PALM have begun to reveal a detailed picture of molecular anatomy in cells at nanoscale level. The techniques are also expected to facilitate the research in neuroscience fields. In this presentation, I will talk about our experiences in STORM-based microscopy of synapses. We have previously developed a technique to visualize glutamate release at single synapse resolutions. Using the glutamate imaging techniques we have successfully determined the quantal parameters that govern the release properties for individual synapses. We combined the glutamate imaging technique with STORM-based superresolution microscopy to uncover molecular anatomy underlying synaptic parameters. Results showed that the number of release sites, which is one of the quantal parameters, matches the number of Mun13-1 clusters within an active zone. This observation led us to hypothesize the Munc13-1 clusters are molecular entity of the release sites. To test this hypothesis we examined the nanoscale localization of syntaxin-1, a SNARE protein, using dual color STORM imaging, and confirmed proximity of these proteins with pair correlation analysis. Further the synaptic recruitment of syntaxin-1 was abrogated by knockdown of Munc13-1. These results indicate that the Munc13-1 nanoclusters constitute the molecular entity of the functional release sites. Thus the superresolution microcopy is a powerful strategy for understanding the relation between functions and molecular anatomy in synapses.