The notochord is a midline mesodermal structure with an essential patterning function in all vertebrate embryos. Zebrafish floating head (flh) mutants lack a notochord, but develop with prechordal plate and other mesodermal derivatives, indicating that flh functions specifically in notochord development. We show that floating head Is the zebrafish homologue of Xnot, a homeobox gene expressed In the amphibian organizer and notochord. We propose that flh regulates notochord precursor cell fate.