The visceral ganglion (VG) comprises the basic motor pool of the swimming ascidian tadpole and has been proposed to be homologous to the spinal cord of vertebrates. Here, we use cis-regulatory modules, or enhancers, from transcription factor genes expressed in single VG neuronal precursors to label and identify morphologically distinct moto- and interneuron subtypes in the Ciona intestinalis tadpole larva. We also show that the transcription factor complement present in each differentiating neuron correlates with its unique morphology. Forced expression of putative interneuron markers Dmbx and Vsx results in ectopic interneuron-like cells at the expense of motoneurons. Furthermore, by perturbing upstream signaling events, we can change the transcription factor expression profile and subsequent identity of the different precursors. Perturbation of FGF signaling transforms the entire VG into Vsx+/Pitx+ putative cholinergic interneurons, while perturbation of Notch signaling results in duplication of Dmbx+ decussating interneurons. These experiments demonstrate the connection between transcriptional regulation and the neuronal subtype diversity underlying swimming behavior in a simple chordate.