The sponges (Porifera) were long thought to have diverged from other animals early.[54] They lack the complex organization found in most other phyla.[55] Their cells are differentiated, but in most cases not organized into distinct tissues.[56] Sponges typically feed by drawing in water through pores.[57] Archaeocyatha, which have fused skeletons, may represent sponges or a separate phylum.[58] However, a phylogenomic study in 2008 of 150 genes in 29 animals across 21 phyla revealed that it is the Ctenophora or comb jellies which are the basal lineage of animals, at least among those 21 phyla. The authors speculate that spongesor at least those lines of sponges they investigatedare not so primitive, but may instead be secondarily simplified.[59] Among the other phyla, the Ctenophora and the Cnidaria, which includes sea anemones, corals, and jellyfish, are radially symmetric and have digestive chambers with a single opening, which serves as both the mouth and the anus.[60] Both have distinct tissues, but they are not organized into organs.[61] There are only two main germ layers, the ectoderm and endoderm, with only scattered cells between them. As such, these animals are sometimes called diploblastic.[62] The tiny placozoans are similar, but they do not have a permanent digestive chamber. The remaining animals form a monophyletic group called the Bilateria. For the most part, they are bilaterally symmetric, and often have a specialized head with feeding and sensory organs. The body is triploblastic, i.e. all three germ layers are well-developed, and tissues form distinct organs. The digestive chamber has two openings, a mouth and an anus, and there is also an internal body cavity called a coelom or pseudocoelom. There are exceptions to each of these characteristics, however for instance adult echinoderms are radially symmetric, and certain parasitic worms have extremely simplified body structures. Genetic studies have considerably changed our understanding of the relationships within the Bilateria. Most appear to belong to two major lineages: the deuterostomes and the protostomes, the latter of which includes the Ecdysozoa, Platyzoa, and Lophotrochozoa. In addition, there are a few small groups of bilaterians with relatively similar structure that appear to have diverged before these major groups. These include the Acoelomorpha, Rhombozoa, and Orthonectida. The Myxozoa, single-celled parasites that were originally considered Protozoa, are now believed to have developed from the Medusozoa as well.

Phylogenetic analysis suggests that the Porifera and Ctenophora diverged before a clade that gave rise to the Bilateria, Cnidaria and Placozoa.[52] Another study based on the presence/absence of introns suggests that Cnidaria, Porifera and Placozoa may be a sister group of Bilateria and Ctenophor Deuterostomes differ from the other Bilateria, called protostomes, in several ways. In both cases there is a complete digestive tract. However, in protostomes, the first opening of the gut to appear in embryological development (the archenteron) develops into the mouth, with the anus forming secondarily. In deuterostomes the anus forms first, with the mouth developing secondarily.[63] In most protostomes, cells simply fill in the interior of the gastrula to form the mesoderm, called schizocoelous development, but in deuterostomes, it forms through invagination of the endoderm, called enterocoelic pouching.[64] Deuterostome embryos undergo radial cleavage during cell division, while protostomes undergo spiral cleavage.[65] All this suggests the deuterostomes and protostomes are separate, monophyletic lineages. The main phyla of deuterostomes are the Echinodermata and Chordata.[66] The former are radially symmetric and exclusively marine, such as starfish, sea urchins, and sea cucumbers.[67] The latter are dominated by the vertebrates, animals with backbones.[68] These include fish, amphibians, reptiles, birds, and mammals.[69] In addition to these, the deuterostomes also include the Hemichordata, or acorn worms.[70] Although they are not especially prominent today, the important fossil graptolites may belong to this group.[71] The Chaetognatha or arrow worms may also be deuterostomes, but more recent studies suggest protostome affinities.