The ems/Emx genes encode homeodomain transcription factors that have conserved actions in anterior embryonic patterning in bilaterian animals ranging from insects to mammals. Recently, genes of the ems/Emx family have been identified in cnidarians raising the possibility that some of their developmental functions might be conserved throughout the Eumetazoa. To determine to what extent functions of a cnidarian ems/Emx protein have been retained across phyla, we carried out cross-phylum rescue expression experiments in which the coral Acropora emx-Am gene was misexpressed in Drosophila ems mutants. Our findings demonstrate that coral emx-Am can substitute for fly ems in embryonic head development and rescue the open head defect and the loss of segmental engrailed expression domains in Drosophila ems mutants. In contrast, the coral emx-Am gene can not substitute for fly ems in embryonic brain development. Even when a hexapeptide motif of the type present in the Drosophila ems gene is inserted into the coral emx-Am gene, rescue of the developmental brain defects in fly ems mutants fails. These findings have implications for understanding the evolutionary origins of head versus brain patterning mechanisms.