Partitioning-defective (Par) genes were originally identified in Caenorhabditis elegans and are involved in asymmetric divisions of the egg. Recently, the expression and function of Par orthologs have been elucidated in deuterostomes, including vertebrates. In this study, we isolated three Par-related genes, Par-1, Par-6, and atypical protein kinase C (aPKC), from the sea urchin Hemicentrotus pulcherrimus and examined their temporal and spatial expression patterns during embryogenesis up to the pluteus stage. All three transcripts existed maternally in eggs and were uniformly expressed in cleavage-stage embryos. From the blastula to early gastrula stages, HpPar-1 expression was transiently restricted to the vegetal plate, including the primary mesenchyme cells (PMCs); this transient reduction was followed by uniform expression. HpPar-6 was expressed uniformly throughout development. In contrast, HpaPKC expression changed dramatically during development. At the blastula stage, HpaPKC expression was restricted to the vegetal region, including PMCs and the vegetal plate. During gastrulation, expression was maintained in PMCs and the archenteron tip, but expression declined at the late gastrula stage. From the prism stage, two cell types started to express HpaPKC: ectoderm cells interspersed in the ciliary band and skeletogenic cells at the posterior end of the larva. At the pluteus stage, the stomach began to express HpaPKC, in addition to the interspersed ciliary band and skeletogenic cells.