Islet-1 (Isl-1) is a LIM domain/homeodomain-type transcription regulator that has been originally identified as an insulin gene enhancer binding protein. Isl-1 is also expressed by subsets of neurons in the central nervous system of rat and chick embryos. We have cloned the Isl-1 cDNA from zebrafish and examined its expression pattern using in situ hybridization to whole-mount embryos. Isl-1 mRNA first appears immediately after gastrulation in the polster, the cranial ganglia, and in Rohon-Beard neurons and ventromedial cells of the spinal cord. The expression by the ventromedial cells is segmentally repeated and becomes restricted to the one or two cells slightly anterior to the segment borders. Double staining by in situ hybridization and an antibody which stains most axons suggested that these segmentally distributed cells may be either the rostral primary motoneuron (RoP) or middle primary motoneuron (MiP). This raises a possibility that Isl-1 may be involved during determination of subtype identities of the primary motoneurons. Furthermore, the specific Isl-1 mRNA expression in the spinal cord is under the control of the somites, since mutant embryo with defective somite failed to maintain this pattern.