The zebrafish homeobox gene floating head (flh) is essential for notochord development and is one of the earliest genes to be expressed in notochord precursors. To understand how flh is regulated during notochord development, we compared the wild-type flh expression pattern to that in embryos mutant for flh and no tail (ntl), the zebrafish homologue of Brachyury. In the early gastrula, the pattern of flh expression is not affected in either flh or ntl mutants, implying that the initial establishment of a gastrula notochord domain is independent of the function of these genes. However, flh RNA is expressed at lower levels in flh mutants suggesting that flh positively regulates its own expression. During gastrulation, flh mutants show an abrupt loss of flh expression in cells which have involuted and entered the hypoblast, while the rest of the expression pattern appears normal, thus flh+ function is specifically required to maintain flh expression in hypoblast cells. The anterior-most part of the notochord rudiment differentially maintains flh expression in both wild types and flh mutant embryos, suggesting that there is unique regulation of flh in this region of the developing notochord. In ntl mutants the spatial pattern of flh expression is altered as early as the late gastrula stage, becoming broad and diffuse. We hypothesize that ntl+ is required for the proper convergence movements of flh-expressing cells.