AbstractMechanisms regulating BMP and Wnt signaling pathways have been widely studied in many organisms. One of the mechanisms by which these pathways are regulated is by binding of extracellular ligands. In the present study, we report studies with two BMP antagonists, gremlin and noggin from Hydra vulgaris Ind-Pune and demonstrate antagonistic relationship between BMP and Wnt pathways. Gremlin was ubiquitously expressed from the body column to head region except in the basal disc and hypostome. During budding, gremlin was expressed predominantly in the budding region suggesting a possible role in budding; this was confirmed in polyps with different stages of buds. Noggin, on the other hand, was predominantly expressed in the endoderm of hypostome, base of the tentacles, lower body column and at the basal disc in whole polyps. During budding, noggin was expressed at the sites of emergence of tentacles suggesting a role in tentacle formation. This was confirmed in alsterpaullone-treated polyps, which showed noggin expression as distinct spots where ectopic organizers and ectopic tentacles eventually formed. Using RT-PCR, we found that up-regulation of Wnt is accompanied with down-regulation of BMP5-8b demonstrating antagonism between the two pathways. Down-regulation of noggin and gremlin, however, occurred only after 24 h recovery. The data suggest that inhibition of BMP pathway by Wnt signaling in hydra does not directly involve noggin and gremlin. Our findings indicate that the BMP/Noggin antagonism evolved early for setting up and/or maintaining the head organizer while involvement of these BMP antagonists during vertebrate axial patterning are recent evolutionary acquisitions.Summary statementWe show that setting up of the Organizer by BMP/Noggin antagonism and role of BMP inhibitors in tissue patterning are evolutionarily ancient, probably arising for the first time in hydra