In the systematic search for phylogenetically conserved proteins in the simplest and most ancient extant metazoan phylum – Porifera, we have identified and analyzed a cDNA encoding the signal recognition particle 54 kD protein (SRP54) from the marine sponge Geodia cydonium (Demospongiae). The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex of a very ancient origin, comprising SRP RNA and several proteins (six in mammals). The nucleotide sequence of the sponge cDNA predicts a protein of 499 amino acid residues with a calculated Mr of 55175. G. cydonium SRP54 displays unusually high overall similarity (90 %) with human/mammalian SRP54 proteins, higher than with Drosophila melanogaster (88 %), or Caenorhabditis elegans (82 %). The same was found for the majority of known and phylogenetically conserved proteins from sponges, indicating that the molecular evolutionary rates in protein coding genes in Porifera as well as in highly developed mammals (vertebrates) are slower, when compared with the rates in homologous genes from invertebrates (insects, nematodes). Therefore, genes/proteins from sponges might be the best candidates for the reconstruction of ancient structures of proteins and genome/proteome complexity in the ancestral organism, common to all multicellular animals.