The engrailed genes play roles in the maintenance of segment polarity in a variety of animals and in the establishment and maintenance of the mid-brain/hind-brain boundary (MHB) in vertebrates. We isolated an ascidian engrailed gene and analyzed its expression pattern during early development. Expression begins at the neurula stage and is restricted to two cells within the neuroectoderm. At the tail-bud stage engrailed-expressing cells are in the "neck" region of the neural tube, which has been proposed to be the ascidian equivalent of the MHB. These same cells also express PAX2/5/8. We speculate that a structure equivalent to the MHB existed before the split of the three chordate sub-phyla.