Echinoids are model organisms in the fields of developmental biology and comparative genomics. They also possess a fossil record of exceptional quality, allowing for detailed studies on the origins of morphological and developmental innovations and their macroevolutionary consequences. However, the relationships among the main lineages of echinoids remain uncertain, as previous efforts have been unable to confidently resolve the oldest nodes in their phylogeny. We perform the first phylogenomic studies of sea urchins, relying on the de novo sequencing and assembly of transcriptomes for many of its distinct lineages. Our effort solve many phylogenetic uncertainties, opening up a new chapter in the study of the evolutionary history of this ancient clade of marine animals.