The ventral branches of the segmental peripheral nerves in the zebrafish embryo are pioneered by the caudal primary (CaP) motor axons, which extend midsegmentally at the interface of the somite and the notochord. The signals that define the CaP pathway are not well understood. To gain insight into the nature of the guidance cues, we have examined the environment of the CaP motor axons by using electron microscopy and histochemistry. Specifically, we have mapped the distribution of the transcription factor engrailed, of a chondrotin sulfate epitope, and of the recognition molecules zebrafish semaphorin z1b and zebrafish tenascin C. Ultrastructural examination of dye-labeled CaP motor axons revealed a close association with the medial surface of the somite but not with the notochord. The CaP axons were always accompanied by cells that appeared to migrate at the interface of somite and notochord. These cells were confined to the posterior half of the somite. Some of the cells may be neural crest derived, many others are probably of sclerotomal origin. The putative migratory cells expressed a chondroitin sulfate epitope that is a marker of sclerotome in the chick. The pathway of the CaP axon and the distribution of the putative neural crest and sclerotome cells correlated with a subdivision of the myotome into an anterior and posterior components, which were evident at the histological level and by the expression of the markers engrailed, semaphorin z1b, chondroitin sulfate, and tenascin C. We suggest that both the pathway choice of the CaP axon and the route of migratory cells reflect this anterior-posterior bipartition of the myotome.