To better understand the phylogeny of extant echinoderms and the placement of Xyloplax, we employed RNA-Seq to retrieve large numbers of orthologous loci from each transcriptome of 40 echinoderm species spanning deep divergences within each of the five extant classes with the aim of discovering orthologous peptide sequences that were well represented in asteroids, holothuroids, echinoids, ophiuroids and crinoids.