The role of the midline floor plate cells in the neuronal differentiation of the spinal cord was examined by comparing putative GABAergic neurons in wildtype zebrafish embryos with those in cyc-1 mutant embryos. The mutation produces a pleiotropic recessive lethal phenotype and is severe in rostral brain regions, but its direct effect in the caudal hindbrain and the spinal cord is apparently restricted to the depletion of the midline floor plate cells. In wildtype embryos, an antibody against the neurotransmitter GABA labeled the cell bodies, axons, and growth cones of three classes of previously identified neurons; dorsal longitudinal neurons (DoLA), commissural secondary ascending neurons (CoSA), and ventral longitudinal neurons (VeLD). A novel ventral cell type, Kolmer-Agduhr (KA) neurons, was also labeled. In the cyc-1 mutant, abnormalities were observed in some, but not all, of the GABAreactive CoSA, VeLD, and KA axons, while the axonal trajectories of DoLA neurons were not affected. Furthermore, the number of KA cells was reduced in the mutant while the numbers of the other GABAreactive cells were unperturbed. These observations corroborate our earlier hypothesis that the floor plate cells are one of several guidance cues that direct axonal outgrowth near the ventral midline of the spinal cord. They also suggest that the floor plate cells may play a role in the cellular differentiation of the spinal cord of zebrafish embryos.