Paxgenes encode a family of transcription factors, many of which play key roles in animal embryonic development but whose evolutionary relationships and ancestral functions are unclear. To address these issues, we are characterizing thePaxgene complement of the coralAcropora millepora, an anthozoan cnidarian. As the simplest animals at the tissue level of organization, cnidarians occupy a key position in animal evolution, and the Anthozoa are the basal class within this diverse phylum. We have identified fourPaxgenes inAcropora: two (Pax-AamandPax-Bam) are orthologs of genes identified in other cnidarians; the others (Pax-CamandPax-Dam) are unique toAcropora. Pax-Aammay be orthologous withDrosophila Pox neuro, andPax-Bamclearly belongs to thePax-2/5/8class. The Pax-Bam Paired domain binds specifically and preferentially to Pax-2/5/8 binding sites. The recently identifiedAcroporagenePax-Dambelongs to thePax-3/7class. Clearly, substantial diversification of thePaxfamily occurred before the Cnidaria/higher Metazoa split. The fourthAcropora Paxgene,Pax-Cam, may correspond to the ancestral vertebratePaxgene and most closely resemblesPax-6. The expression pattern ofPax-Cam, in putative neurons, is consistent with an ancestral role of thePaxfamily in neural differentiation and patterning. We have determined the genomic structure of eachAcropora Paxgene and show that some splice sites are shared both between the coral genes and between these andPaxgenes in triploblastic metazoans. Together, these data support the monophyly of thePaxfamily and indicate ancient origins of several introns.