Cyclooxygenase is a key enzyme in prostanoid biosynthesis. Mammalian species have two cyclooxygenases, constitutively expressed cyclooxygenase-1 (Cox-1) and inducible cyclooxygenase-2 (Cox-2). Cox-1 and/or Cox-2 have been also identified in other vertebrates, including fish. We identified a second zebrafish Cox-2 gene orthologue, Cox-2b. All of the functionally important amino acids for cyclooxygenase enzymes are conserved in Cox-2b. The 3' untranslated region of the Cox-2b message contains AU rich elements characteristic of regulation at the level of mRNA stability. Constitutive tissue expression patterns for Cox-2a and Cox-2b are distinct, but overlap. Both Cox-2a and Cox-2b expression are inducible in the kidney when fish are exposed to tetradecanoylphorbol acetate. Like Cox-2a, Cox-2b protein, expressed in COS cells is functionally active. Thus, the zebrafish genome contains two functional, inducible Cox-2 genes. Database searching demonstrates that some fish genomes contain multiple Cox-1 or Cox-2 cyclooxygenase genes, suggesting alternate duplication and retention of this gene.