Optogenetic techniques provide effective ways of manipulating the functions of selected neurons with light. In the current study, we engineered an optogenetic technique that directly inhibits neurotransmitter release. We used a genetically encoded singlet oxygen generator, miniSOG, to conduct chromophore assisted light inactivation (CALI) of synaptic proteins. Fusions of miniSOG to VAMP2 and synaptophysin enabled disruption of presynaptic vesicular release upon illumination with blue light. In cultured neurons and hippocampal organotypic slices, synaptic release was reduced up to 100%. Such inhibition lasted >1 hr and had minimal effects on membrane electrical properties. When miniSOG-VAMP2 was expressed panneuronally in Caenorhabditis elegans, movement of the worms was reduced after illumination, and paralysis was often observed. The movement of the worms recovered overnight. We name this technique Inhibition of Synapses with CALI (InSynC). InSynC is a powerful way to silence genetically specified synapses with light in a spatially and temporally precise manner. •MiniSOG mediates CALI of presynaptic release proteins•Synaptic release is inhibited optogenetically with miniSOG fused VAMP2 or SYP1•Light reversibly reduces movement in miniSOG-VAMP2-expressing C. elegans Lin et al. tether miniSOG to presynaptic proteins allowing optogenetic inhibition of synaptic release. This technique, InSynC, effectively inhibits synapses in cultured neurons, organotypic slice, and behaving C. elegans and is useful for studying the function of specific projections.