Zebrafish semaphorin 1b (sema Z1b) is a new member of the semaphorin family, related to mammalian sema D/III. It is expressed in rhombomeres three and five, and in the posterior half of newly formed somites which is avoided by ventrally extending motor axons. Embryos injected at the 1-2 cell stage with synthetic sema Z1b mRNA developed normally but many (63%) showed missing or severely stunted ventral motor nerves. Other axons, somites, and hindbrain rhombomeres were not affected. No abnormalities were seen in control embryos injected with lacZ mRNA. Sema Z1b might normally influence the midsegmental pathway choice of the ventrally extending motor axons by contributing to a repulsive domain in the posterior somite.