Hydra is a classical model organism to understand fundamental developmental biological processes such as regeneration and axis formation. Here, we show that two genes which share some similarity with members of the Dickkopf family of proteins, HyDkk1/2/4-A and HyDkk1/2/4-C, are co-expressed in gland cells and regulated by the positional value gradient. While HyDkk1/2/4-A is expressed throughout the gastric region, HyDkk1/2/4-C has a graded expression pattern with a high level of transcripts just below the tentacle zone and absence of expression in the budding zone. Blocking the activity of GSK-3beta caused a drastic downregulation of HyDkk1/2/4-C expression in the gastric tissue. Experimental reduction of the number of HyDkk1/2/4-C-expressing cells resulted in expansion of the HyWnt expression domain in the hypostome. Thus, similar to Dickkopf proteins in vertebrates, one of the functions of HyDkk1/2/4-C in hydra may be to antagonize Wnt signalling.