In vertebrates, embryonic structures present at the dorsal midline, prechordal plate, notochord, hypochord and floor plate share a common embryonic origin. In zebrafish, they derive from a pool of progenitors located within the embryonic shield at the onset of gastrulation. The molecular mechanisms responsible for the common development of these structures remain unknown. Based on their spatial and temporal expression, transcription factors of the Forkhead box A (FoxA) family appeared to be good candidates to play such a role. In agreement with this hypothesis, we found that simultaneous knockdown of FoxA2 and FoxA3 abolish the formation of all axial derivatives, while overexpression of these transcription factors strongly enlarges dorsal mesodermal territories. We establish that, in FoxA2-FoxA3 double morphants, precursors of axial tissues are correctly induced at early gastrula stage, but their dorsal midline identity is not maintained during development and we found that progenitors of these tissues are cell-autonomously re-specified to form muscle fibers as well as cells of the ventral neural tube. Our study provides the first example of a specific loss of all dorsal midline tissues and demonstrates that members of the FoxA family have redundant functions essential to maintain the axial identity of prechordal plate, notochord, floor plate and hypochord progenitors during gastrulation.