The auricularia larva of sea cucumbers and tornaria larva of acorn worms share striking developmental and morphological similarities. They are regarded as not only an archetype of the nonchordate deuterostome larva, but also an archetype of the origin of chordates. Here we report the characterization and spatial expression patterns of the BMP-2/4 genes of a hemichordate acorn worm (Pf-bmp2/4) and an echinoderm sea cucumber (Sj-bmp2/4). Both the Pf-bmp2/4 and Sj-bmp2/4 genes exhibited apparently conserved expression in the region of the coelomopore complex. This is in agreement with the homology between their basic larval body plans with respect to coelomogenesis and allows us to discuss the evolutionary counterparts of the coelomopore complex in chordates.