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Chemical neurotransmission is central to neurotypical brain function but also implicated in a variety of psychiatric neurodegenerative diseases. The release dynamics of neurotransmitters is correlated with but distinct from neuronal electrical signal propagation. It is therefore necessary to track neurotransmitter modulation separately from neuron electrical activity. Here, we present a new approach for imaging deuterated neurotransmitter molecules with stimulated Raman scattering (SRS) microscopy. Using SRS microscopy, we perform direct imaging of deuterated dopamine and GABA in PC12 chromaffin cells, and in primary hippocampal neurons, respectively, based on the carbon-deuterium vibrational frequencies. We demonstrate that SRS imaging of these isotopologues directly visualizes intracellular neurotransmitters without changing the neurotransmitters' chemical identity and requiring custom synthesis or genetic encoding protocols. We further show that stimulation of neurotransmitter release results in an overall 20-50 percent intracellular neurotransmitter signal reduction, in agreement with comparable neurotransmission dynamics studies, with the ability to observe inter- and intracellular variation in vesicular neurotransmitter release. Taken together, our data suggest that neurotransmitter isotopologues can serve as a commercially-available, biocompatible, and generalizable method to image neurotransmitters with deuterated molecules that are virtually chemically identical to their native counterparts.