The invertebrate chordate Ciona can provide clues about the origins of the vertebrate nervous system. The Ciona caudal nerve cord has similar anatomical features to the vertebrate spinal cord, but it is reported to lack motor neurons or contain ill-defined neurons. Here, William Smith and colleagues identify functional motor neurons in the Ciona larval tail by looking at a later developmental stage than previous studies. Using in situ hybridisation, the researchers observe the presence of cholinergic neurons in the caudal nerve cord. These neurons also express the motor neuron-specific transcription factor mnx. Next, they conduct functional assessments of these putative motor neurons and observe muscle contraction in the tail when the neurons are stimulated optogenetically. Comparing the positions of the motor neurons detected by in situ hybridisation and the published Ciona connectome data, the researchers confirm that the neurons connect to muscle cells and form neuromuscular junctions. Furthermore, they map out the synaptic connections and find that the motor neurons form pre-synaptic contacts with other neurons and components of sensorimotor circuits. Collectively, the findings indicate the presence of motor neurons in the Ciona caudal nerve cord, suggesting homology to the vertebrate spinal cord.