► Motor neurons have undergone sequential changes in their organization in the spinal cord in accordance with the emergence of their peripheral targets. ► The appearance of the Hox-dependent LMCs seems to be linked to the emergence of paired limbs. ► In the lineage of actinopterygian fishes, a Hox-dependent LMC has not been acquired. ► Primitive pectoral innervation has shown to be originated from both the hindbrain and the spinal cord. ► The Hox-dependent mechanism of appendicular innervation has not been established with regard to pelvic fin innervation.