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Complex neocortical functions rely on networks of diverse excitatory and inhibitory neurons. While local connectivity rules between major neuronal subclasses have been established, the specificity of connections at the level of transcriptomic subtypes remains unclear. We introduce single transcriptome assisted rabies tracing (START), a method combining monosynaptic rabies tracing and single-nuclei RNA sequencing to identify transcriptomic cell types, providing inputs to defined neuron populations. We employ START to transcriptomically characterize inhibitory neurons providing monosynaptic input to 5 different layer-specific excitatory cortical neuron populations in mouse primary visual cortex (V1). At the subclass level, we observe results consistent with findings from prior studies that resolve neuronal subclasses using antibody staining, transgenic mouse lines, and morphological reconstruction. With improved neuronal subtype granularity achieved with START, we demonstrate transcriptomic subtype specificity of inhibitory inputs to various excitatory neuron subclasses. These results establish local connectivity rules at the resolution of transcriptomic inhibitory cell types. • START combines monosynaptic rabies tracing with single-nucleus RNA sequencing • Local cortical circuit connectivity is transcriptomic subclass and subtype specific • Excitatory neurons receive selective input from subtypes of Sst/Pvalb/Vip/Lamp5 neurons • Transcriptomic characterization of inhibitory input neurons reveals new circuit motifs Patiño et al. introduce single transcriptome assisted rabies tracing (START), a new technical approach combining transsynaptic neuronal circuit mapping with transcriptomic classification to achieve precise neuronal characterization. Using START, they identify novel local cortical circuit connectivity motifs between inhibitory neuron subtypes and layer-specific excitatory subclasses. [ABSTRACT FROM AUTHOR]