Cnidarians are the only non-bilaterian group to evolve ciliated larvae with an apical sensory organ integrated with neurons, possibly homologous to the bilaterians. Within cnidarians, an apical organ with a ciliary tuft is identified only in sea anemones. Whether this apical tuft has evolved independently in anthozoans or alternatively originated in the eumetazoans and was lost independently in specific groups of cnidarians and bilaterians is uncertain. Overall design: Here, we generated transcriptomes of the apical domain during the planula stage of four species representing three key groups of cnidarians: Aurelia aurita (medusozoan Scyphozoa), Nematostella vectensis (Actiniaria), and Acropora millepora & Acropora tenuis (Scleractinia). Using an ortholog-analysis approach, we revealed the active and dynamic anteroposterior gene regulatory network in all three cnidarian groups.