The process of neural crest cell migration differs between the lamprey and swordtail [Hirata et al., Zoological Science 14: 305-312 (1997)]. In swordtail embryos, neural crest cells in the ventral pathway are distributed ventrally beyond the notochord at all axial levels of the trunk. In contrast, no neural crest cells are seen ventrally beyond the notochord in post-branchial regions of lamprey embryos, although in the branchial regions some cells migrate ventrally beyond the notochord. Since sclerotomal development is essential in the formation of ventral pathways in avian and mammalian embryos, sclerotomal development in lamprey and swordtail embryos was examined to understand the mechanism underlying the differences in neural crest cell migration between these two animals. Sclerotomal development and neural crest cell migration progressed concurrently in the swordtail trunk. In the lamprey, the formation of the sclerotome was regionally different along the antero-posterior axis. In the branchial region, where neural crest cells are observed ventrally beyond the notochord, sclerotomal development was closely correlated with neural crest cell migration as in the swordtail. The overt sclerotome was not observed in the lamprey trunk posterior to the branchial region during the period of neural crest cell migration. These observations suggest that differences in the timing of neural crest cell migration and sclerotomal development generate the differences in migration of lamprey and swordtail neural crest cells along the ventral pathways. Heterochronic differences in sclerotomal development correlated with neural crest cell migration may have some significance in the evolution of the trunk body organization from agnathans to gnathostomes.