Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of unidscovered evolutionary history of the crown in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two.