Many basic helix-loop-helix transcriptional factors play important roles in vertebrate neurogenesis. Among them, Neurogenins act as determination factors and initiate the expression of differentiation genes such as neuroD and other neurogenic genes. Here we describe a zebrafish cDNA (neurogenin3 or ngn3) encoding a novel member of the Neurogenin family closest to mouse Ngn3 and human NGN3. Using a zebrafish radiation hybrid panel, ngn3 was mapped to zebrafish linkage group 13 and the region displayed a conserved synteny with the region of human chromosome 10 containing NGN3. As judged by RT-PCR and whole-mount in situ hybridization, ngn3 expression in zebrafish started much later than other neurogenin genes, at only around 24 h post-fertilization (hpf) and with a higher level of expression on the left side of the anterio-ventral diencephalon. Later at 48 hpf, ngn3 expression was detected in a small number of cells in the tuberal hypothalamus. Unlike Ngn3 in the mouse, zebrafish ngn3 mRNAs were not detected in developing pancreas and spinal cord. Genomic Southern blot hybridization suggested that a closely related sequence is present in the zebrafish genome and the hypothetical gene might result from the recent genome duplication in certain teleost lineage and share the function of the common ancestor with the currently characterized ngn3.