Using the polymerase chain reaction, we identified four different homeobox-containing genes in Hydra magnipapillata. Three of them, cnox1-Hm, cnox2-Hm and cnox4-Hm, were equivalent to homeobox genes that had already been identified in other species of cnidarians. cnox5-Hm was a new homeobox gene and was very similar to Mox1 in the mouse. Together with the published data, our results indicate that there are at least eight distinct classes of homeobox genes in cnidarians. These homeobox genes show a maximum of 60 to 77% identity in terms of the amino acid residues in their homeodomains to certain classes of homeobox genes that have been identified in Drosophila.