Embryonic development in metazoan animals involves a remarkable degree of both genetic and epigenetic regulation. Polycomb group (PcG) genes are essential for initiation and maintenance of epigenetic developmental regulation. This report identifies homologous PcG genes representing the core components of three known Polycomb repressive complexes in the sea urchin Strongylocentrotus purpuratus. Quantitative, temporal, and spatial analyses revealed two significant aspects of their transcript expression during embryonic development. First, almost all showed a localized expression pattern in mesenchyme blastula and gastrula-stage embryos. As the embryo specifies its three germ layers, it may require its PcG gene transcripts to remain in localized stem cell populations, but turn-over in differentiating tissues. Second, their transcript levels gradually decreased during larval pluteus stages. This finding is consistent with progressive cell differentiation in the embryo. Taken together, these results suggest that PcG genes are conserved in S. purpuratus and are actively expressed during early embryogenesis.