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Abstract Many species in the tunicate family Molgulidae have independently lost their swimming larval form and instead develop as tailless, immotile larvae. These larvae do not develop structures that are essential for swimming such as the notochord, otolith, and tail muscles. However, little is known about neural development in these nonswimming larvae. Here, we studied the patterning of the Motor Ganglion (MG) ofMolgula occulta, a nonswimming species. We found that spatial patterns of MG neuron regulators in this species are conserved, compared with species with swimming larvae, suggesting that the gene networks regulating their expression are intact despite the loss of swimming. However, expression of the key motor neuron regulatory geneEbf (Collier/Olf/EBF)was reduced in the developing MG ofM. occultawhen compared with molgulid species with swimming larvae. This was corroborated by measuring allele‐specific expression ofEbfin hybrid embryos from crosses ofM. occultawith the swimming speciesM. oculata. Heterologous reporter construct assays in the model tunicate speciesCiona robustarevealed a specificcis‐regulatory sequence change that reduces expression ofEbfin the MG, but not in other cells. Taken together, these data suggest that MG neurons are still specified inM. occultalarvae, but their differentiation might be impaired due to reduction ofEbfexpression levels.