Many of the characteristics that make vertebrates so different from other animals relate to the head, with its distinct cranium and specialized eyes and ears. The form of the head is in large part specified by neural crest cells which arise from the neural plate, the region of the embryo that forms the central nervous system, and migrate through the body to contribute to a variety of tissues. The origin of the neural crest has been a mystery. This study shows that a distant relative of vertebrates, the solitary sea squirt Ciona intestinalis, has a lineage of cells originating at the margin of the neural plate. These cells express several neural crest specification genes, but lack some of the defining properties of neural crest, such as long-range migration. However, targeted misexpression of the regulatory gene Twist is sufficient to induce some of these properties. The results suggest that much of the neural crest gene network predated the divergence of tunicates and vertebrates, and that the co-option of mesenchyme determinants, such as Twist, into the neural plate ectoderm was crucial for the emergence of the vertebrate 'new head'.