The micromere gene regulatory network (GRN) has been extensively examined using sea urchins belonging to the order Echinoida. To examine whether the network of Echinoida species is conserved in Scaphechinus mirabilis, an irregular echinoid of the order Clypeasteroida, the genes micro1, hesC, alx1, ets1, and delta were isolated from S. mirabilis and their expression patterns were compared with those from Hemicentrotus pulcherrimus, a species belonging to the order Echinoida. Data from this study suggest that the early GRN architecture had been largely established in a common ancestor of these two species. On the other hand, we found vegetal shifts in expression domains of some GRN members in H. pulcherrimus embryos compared to S. mirabilis embryos. Developmental Dynamics 239:3391-3403,