Cnidarians (corals, sea anemones, hydroids, and jellyfish) are a basal taxon closely related to bilaterally symmetrical animals [1-3] and have been characterized as diploblastic and as radially symmetrical around their longitudinal axis. We show that some orthologs of key bilaterian dorso/ventral (D/V) patterning genes, including the TGF beta signaling molecules NvDpp and NvBMP 5-8 and their antagonist NvChordin, are initially expressed asymmetrically at the onset of gastrulation in the anthozoan sea anemone Nematostella vectensis. Surprisingly, unlike flies and vertebrates, the TGF beta ligands and their antagonist are colocalized at the onset of gastrulation but then segregate by germ layer as gastrulation proceeds. TGF beta ligands, their extracellular enhancer, NvTolioid, and components of their downstream signaling pathway (NvSmad1/5 and NvSmad4) are all coexpressed in presumptive endoderm, indicating that only planar TGF beta signaling operates at these stages. NvChordin expression forms a boundary between TGF beta-expressing endodermal cells and aboral ectoderm. Manipulation of nuclear beta-catenin localization affects TGF beta ligand and antagonist expression, suggesting that the ancestral role of the dpp/chordin antagonism during gastrulation may have been in germ-layer segregation and/or epithelial patterning rather than dorsal/ventral patterning.