While the enteric nervous system (ENS) of jawed vertebrates is largely derived from the vagal neural crest, lamprey are jawless vertebrates that lack the vagal neural crest, yet possess enteric neurons derived from late-migrating Schwann cell precursors. To illuminate homologies between the ENS of jawed and jawless vertebrates, here we examine the diversity and distribution of neuronal subtypes within the intestine of the sea lamprey during late embryonic and ammocete stages. In addition to previously described 5-HT-immunoreactive serotonergic neurons, we identified NOS and VIP neurons, consistent with motor neuron identity. Moreover, the presence of Calbindin neurons was suggestive of sensory IPANs. Quantification of neural numbers by subtype across the length of the intestine revealed significant, albeit subtle differences in distribution of neuronal markers at different axial levels, suggesting that the complex organizational features of the ENS may have emerged much earlier in the vertebrate lineage than previously appreciated.