In vertebrates, COX-1 and COX-2, two cyclooxygenase isozymes with different physiological functions and gene regulation, catalyze identical reactions in prostaglandin synthesis. It is still not understood why there are multiple forms of COX enzyme in the same cell type and when the evolutionary duplication of the COX gene occurred. Here we report the structure of two genes encoding for COX isozymes in the coral Gersemia fruticosa, the first non-vertebrate organism from which a cyclooxygenase was characterized. Both genes are about 20 kb in size and consist of nine exons. Intron/exon boundaries are well conserved between coral and mammalian COX genes. mRNAs of the previously reported G. fruticosa COX-A (GenBank TM accession number AY004222) and the novel COX-B share 94% sequence identity in the coding regions and less than 30% in the 5-and 3-untranslated region. Transcripts of both COX genes are detectable in coral cells, although the transcriptional level of COX-A is 2 orders of magnitude higher than COX-B. Expression of both coral genes in mammalian cells gave functional proteins with similar catalytic properties. By data base analyses we also detected and constructed different pairs of COX genes from the primitive chordates, Ciona savignyi and Ciona intestinalis. These two gene pairs encode proteins with 50% intra-species and only 70% cross-species sequence identity. Our results suggest that invertebrate COX gene pairs do not correspond to vertebrate COX-1 and COX-2 and are consistent with duplication of the COX gene having occurred independently in corals, ascidians, and vertebrates. It is evident that due to the importance and complexity of its regulatory role, COX has multiple isoforms in all organisms known to express it, and the genes encoding for the isozymes may to be regulated differently.Prostaglandins are important signaling molecules that are involved in inflammation, ovulation, modulation of immune responses, and mitogenesis. The key enzyme in prostaglandin biosynthesis is prostaglandin-endoperoxide G/H synthase (EC 1.14.99.1), commonly known also as cyclooxygenase (COX) 1 (1, 2). Vertebrates from fish to human beings have two different COX isozymes, COX-1 and COX-2 (3-6). COX-1 is constitutively expressed in most mammalian tissues, and expression levels of this enzyme do not vary greatly in adult animals. COX-2, although absent in most cells, can be rapidly induced in many cell types by inflammatory cytokines, growth factors, and tumor promoters (2, 7). Mammalian COX isozymes are encoded by separate single copy genes that map to distinct chromosomes (1, 8). The human gene for COX-1 is ϳ22 kb in length with 11 exons and is transcribed as 2.8-and 5.2-kb mRNA (9, 10). The gene for COX-2 is about 8.3 kb long with 10 exons, and it is transcribed as 2.8-and 4.6-kb mRNA variants (11-15). The gene structures of COX-1 and COX-2 demonstrate remarkable conservation of exon/intron junctions (16 -19). The main differences between the COX-1 and COX-2 genes consist of different intron lengths and one missing int...