We have isolated cDNA clones and polymerase chain reaction products containing the entire coding region for nuclear pore complex protein p62 of a lower metazoan, the freshwater polyp Hydra vulgaris (Hv), and compared the deduced amino acid (aa) sequence with those of the vertebrate and yeast homologues. The open reading frame defines a protein of 534 aa, corresponding to a molecular mass of 56,072 Da and an isoelectric point (pI) of 5.0. Secondary structure predictions revealed the division into two domains, as previously observed in vertebrate p62: the N-terminal domain (aa 1-338) with a pI of 10.7 contains the evolutionarily conserved repeated pentapeptide motif, XFXFG, known from several nucleoporins, a low content of charged aa (3.25%) and a high degree of hydroxy aa (40.2%). Otherwise, sequence identity between the N-terminal domains of p62 from Hv and various vertebrates is rather low (28-34%). By contrast, the C-terminal domain with a pI of 4.6 is richer in charged aa (36.7%), exhibits heptad repeats typical for alpha-helices organized in coiled-coils and shows a high sequence identity with amphibian (53%) and mammalian p62 (55%). Differences and similarities between p62 of Hv and vertebrates, and between Hv p62 and its putative homologues from the budding yeast, Saccharomyces cerivisiae, and the fission yeast, Schizosaccharomyces pombe, are discussed.