Recent studies of molecular phylogeny based upon comparisons of the partial nucleotide sequences of 18 and 28S rRNAs have suggested that the metazoa are polyphyletic, i.e., that diploblasts (poriferans, cnidarians, ctenophores, and placozoans) and triploblasts form two separated monophyletic units. In order to examine this hypothesis, we determined almost the complete sequences of small subunit (18S-like) rDNA for two poriferans and a ctenophore. Phylogenetic comparisons of the sequences, together with those of a cnidarian, triploblasts and other eukaryotes, supported the monophyly of the metazoa. Among the diploblasts, the ctenophore showed some similarities to the poriferans.