The T-Box transcription factor Brachyury plays important roles in the development of all bilateral animals examined so far. In order to understand the ancestral function of Brachyury we cloned NemBra1, a Brachyury homolog from the anthozoan sea anemone Nematostella vectensis. Anthozoa are considered the basal group among the Cnidaria. First NemBra1 expression could be detected at the blastula/gastrula transition and gene activity persists until adulthood of the animals. In situ hybridization shows that NemBra1 expression in gastrulae and early planula larvae is restricted to a circle around the blastopore. When the larvae begin to metamorphose into primary polyps, the expression zone extends into the developing mesenteries. In adult polyps Brachyury expression persists in the mesenteries, but is excluded from the septal filament and the differentiated retractor muscles, which also develop from the mesenteries. We conclude that the ancestral function of Brachyury was in specifying the blastopore and its endodermal derivatives.