Sponges (Porifera) are the simplest representatives of the animal kingdom which have separated first from other Metazoa. First systematic genomic studies of sponges have shown that they possess a highly complex genome which has already existed at the common ancestor of all multicellular animals (Urmetazoa). Molecular-genetic characterization, as well as reconstruction of the endemic stygobitic sponge Eunapius subterraneus phylogeny, exclude this sponge from genus Eunapius and indicate the existence of a relevant inconsistency of the classic sponge taxonomy with the one obtained by molecular-genetic methods. Random sequencing of the cDNA (complementary DNA) library of the E. subterraneus has created a preliminary EST library (expressed sequence tags), which was then analyzed by bioinformatics tools. This analysis has allowed further investigation of sponge genes and proteins in comparison with genes and proteins from other organisms. These results have confirmed the hypothesis in which the common ancestor of all Metazoa had already had unusually complex genome, as well as that there is a surprisingly high similarity between sponge and human proteins. A complete cDNA coding for a selenoprotein W was obtained from the cDNA library. Primary structure analysis showed highly conserved coding regions and SECIS motifs in noncoding region.