The configuration of the ascidian tadpole larva represents the most simplified and primitive chordate body plan. The present study revealed that Ciona intestinalis contains two hedgehog genes (Ci-hh1 and Ci-hh2), which are likely to be independent duplicate genes in this animal and ancestral to the three types of hedgehog gene of vertebrates. Ci-hh1 was expressed maternally and its maternal transcript was distributed evenly in fertilized eggs and early embryos. Ci-hh2 was expressed zygotically in the tailbud embryo and its transcript was evident only in cells of the ventral nerve cord. The notochord cells did not express the hedgehog genes in Ciona embryos.