We report the cDNA sequence encoding Ub52 from the cnidarian Acropora millepora. As in other eukaryotes, the N-terminal region of the deduced amino-acid sequence is a ubiquitin moiety and the C-terminal region CEP52, a protein component of the large ribosomal subunit. A millepora Ub52 is highly homologous (> 95% identical) with the corresponding Drosophila and vertebrate sequences, the cnidarian sequence having higher identity with these 'higher' metazoan homologs than does the corresponding Caenorhabditis elegans protein. However, the cnidarian sequence contains two unique substitutions in the ubiquitin moiety, Ser22 and Thr28. Northern analysis indicates that A. millepora Ub52 is encoded by a small (< 800 nt) mRNA present in eggs and is first expressed after the early gastrula stage in embryonic development.