Echinoderms are an exceptional group in bilaterians in that they develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on progeny of the earliest-diverged deuterostome, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster genes reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages was not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameral axes development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 mya.