Echinoderms are marine invertebrates but are phylogenetically much more related to the chordates, to which we belong, than are other invertebrate model organisms like Drosophila or C. elegans. The recently available sequence of the sea urchin genome offers an opportunity to draw an inventory of the developmental genes represented in a non-chordate deuterostome and to compare this complement with that present in vertebrates and other invertebrates. In the first part of this review, we draw an inventory of the genes acting in the TGF-β signal transduction pathway and describe the sea urchin complement of ligands, receptors, Smads, extracellular modulators and transcriptional regulators present in the genome of the purple sea urchin Strongylocentrotus purpuratus. In the second part of this review, we describe the results of recent studies addressing the function of some of these TGF-β during sea urchin embryogenesis. Finally, we discuss hypotheses regarding a possible ancestral function of the Nodal/Lefty signalling pathway in deuterostomes.