In a classic study with silver staining methods, the somatomotor system of the amphioxus spinal cord was described as consisting of three different types of neuron segmentally arranged in two opposite fan-shaped group types (Bone [1960] J Comp Neurol 115:27-64). The present study reports the presence of calretinin-like immunoreactivity in the somatomotor system of the amphioxus, which allows us to reevaluate old descriptions of amphioxus motoneurons. In the spinal cord, two types of calretinin-like immunoreactive (CR-ir) motoneurons, large and small, sent processes toward the ventrolateral region of the cord, where they branched and gave rise to processes coursing longitudinally in the somatomotor bundles. These processes produced a number of long and thin collaterals directed to several neuropil regions. Short collaterals were directed to the region of the neuromuscular contacts at the ventrolateral surface of the cord. The groups of CR-ir motoneurons exhibited a segmental organization and were localized only facing the myomeres, i.e., opposite to the entrance of the dorsal nerve roots, which is at variance with the above-mentioned classical report. CR-ir motoneurons were also observed in the brain between a level just rostral to the nerve III entry and nerve VI. The CR-ir somatomotor bundle ascended to the region of the neuromuscular junction of myomere 1. Additional faintly CR-ir neurons were observed in the region of the lamellate body of the brain. Our results reveal for the first time that calretinin immunoreactivity in the central nervous system of amphioxus was limited to a few types of neuron and that calretinin was not expressed in the peripheral nervous system, unlike vertebrates.