Six alternative hypotheses for the phylogenetic origin of Bilateria are evaluated by using complete 18S rRNA gene sequences for 52 taxa. These data suggest that there is little support for three of these hypotheses. Bilateria is not likely to be the sister group of Radiata or Ctenophora, nor is it likely that Bilateria gave rise to Cnidaria or Ctenophora. Instead, these data reveal a close relationship between bilaterians, placozoans, and cnidarians. From this, several inferences can be drawn. Morphological features that previously have been identified as synapomorphies of Bilateria and Ctenophora, e.g., mesoderm, more likely evolved independently in each clade. The endomesodermal muscles of bilaterians may be homologous to the endodermal muscles of cnidarians, implying that the original bilaterian mesodermal muscles were myoepithelial. Placozoans should have a gastrulation stage during development. Of the three hypotheses that cannot be falsified with the 18S rRNA data, one is most strongly supported. This hypothesis states that Bilateria and Placozoa share a more recent common ancestor than either does to Cnidaria. If true, the simplicity of placozoan body architecture is secondarily derived from a more complex ancestor. This simplification may have occurred in association with a planula-type larva becoming reproductive before metamorphosis. If this simplification took place during the common history that placozoans share with bilaterians, then placozoan genes that contain a homeobox, such as Trox2, should be explored, for they may include the gene or genes most closely related to Hox genes of bilaterians.Despite numerous speculations and analyses concerning the evolutionary relationships of the major animal clades, until recently only three distinct hypotheses have been offered concerning the phylogenetic position of Bilateria within the other basal metazoan groups (Fig. 1 A-C). Two of these hypotheses are commonly found in zoology textbooks. One view, an idea that goes back to Haeckel (1) and was championed by Hyman (2, 3), is that Bilateria is the sister group to Radiata (Cnidaria and Ctenophora). A second hypothesis, preferred by Harbison (4) and Wilmer (5), holds that Bilateria and Ctenophora share a more recent common ancestor than either does to Cnidaria. Recent cladistic studies based on morphological characters (6, 7) have supported this second view. A third alternative, which appears to have fallen out of favor, has Bilateria as a nonmonophyletic group, with both cnidarians and ctenophorans derived from flatworm ancestors (8). The strength of these hypotheses is difficult to weigh on morphological evidence alone. The diploblastic groups have disparate body plans with many derived features, only a few of which are potentially informative as to their relative phylogenetic positions. Furthermore, homoplasies are difficult to infer when dealing with such general features as mouths, mesoderm, and symmetry.Molecular sequence studies provide sets of characters that can be used to both evaluate previ...