The notochord plays a central role in vertebrate development, acting as a signalling source that patterns the neural tube and somites. In in vitro assays, the secreted protein Sonic hedgehog mimics the inducing effects of notochord on both presomitic mesoderm and neural plate explants of amniote embryos, suggesting that both patterning activities of the notochord may be mediated by this protein in vivo. In zebrafish, however, mutants with disrupted notochord development lack a specific muscle cell type, the muscle pioneers, although they retain the ability to induce neural differentiation, raising the possibility that neural tube and somite patterning may be mediated by distinct signals. Here we describe a new member of the hedgehog family, echidna hedgehog, that is expressed exclusively in the notochord and has the ability to rescue the differentiation of muscle pioneer cells in mutants with no notochord. Moreover, we show that a combination of ectopic echidna hedgehog and sonic hedgehog expression induces supernumary muscle pioneers in wild-type embryos, suggesting that both signals act sequentially to pattern the developing somites.