The hypothetical last common ancestor of all bilateria is termed the "Urbilaterian". The nature of the first bilaterian is a matter of debate. One side suggests that acoelomates gave rise to the other groups (planuloid-aceloid hypothesis by von Graff, Metchnikoff, Hyman, or Salvini Plawen), while the other poses that the first bilaterian was a coelomate organism and the main acoelomate phyla (flatworms and gastrotrichs) have lost body cavities secondarily (the Archicoelomata hypothesis and its variations such as the Gastrea by Haeckel or Sedgwick, the Bilaterosgastrea by Jägersten, or the Trochaea by Nielsen).
The first evidence of bilateria in the fossil record comes from trace fossils in Ediacaran sediments, and the first bona fide bilaterian fossil is Kimberella, dating to 555million years ago. Earlier fossils are controversial; the fossil Vernanimalcula may be the earliest known bilaterian, but may also represent an infilled bubble.Fossil embryos are known from around the time of Vernanimalcula (580million years ago), but none of these have bilaterian affinities. Burrows believed to have been created by bilaterian life forms have been found in the Tacuarí Formation of Uruguay, and are believed to be at least 585 million years old.
There are two or more superphyla (main lineages) of Bilateria. The deuterostomes include the echinoderms, hemichordates, chordates, and possibly a few smaller phyla. The protostomes include most of the rest, such as arthropods, annelids, mollusks, flatworms, and so forth. There are a number of differences, most notably in how the embryo develops. In particular, the first opening of the embryo becomes the mouth in protostomes, and the anus in deuterostomes. Many taxonomists now recognize at least two more superphyla among the protostomes, Ecdysozoa (molting animals) and Lophotrochozoa. Within the latter, some researchers also recognize another superphylum, Platyzoa, while others reject the Platyzoa monophyly. The arrow worms (Chaetognatha) have proven particularly difficult to classify, with some taxonomists placing them among the deuterostomes and others placing them among the protostomes. The two most recent studies to address the question of chaetognath origins support protostome affinities.
A phylogeny of the Bilateria after Nielsen (2001) is as follows.[nb 1].
^Knoll, Andrew H. and Sean B. Carroll. (1999) Early Animal Evolution: Emerging Views from Comparative Biology and Geology. Science. 25 June 1999: Vol. 284. no. 5423, pp. 2129–2137. Found at  — URL retrieved November 15, 2006
^Balavoine, Guillaume, & Adoutte, Andre. 2003. The segmented Urbilateria: A testable scenario. Integrative & Comparative Biology 43: 137–147. Found at  — URL retrieved November 15, 2006
^Aubet, Natalie R., et al. (June 29, 2012). "Bilaterian burrows and grazing behavior at >585 million years ago". Science (American Association for the Advancement of Science) 336 (6089): 1693+. doi:10.1126/science.1216295.
^ abHalanych, K.; Bacheller, J.; Aguinaldo, A.; Liva, S.; Hillis, D.; Lake, J. (17 March 1995). "Evidence from 18S ribosomal DNA that the lophophorates are protostome animals". Science267 (5204): 1641–1643. doi:10.1126/science.7886451. PMID7886451.Cite uses deprecated parameters (help)
^Paps, J.; Baguna, J.; Riutort, M. (14 July 2009). "Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and Supports a Paraphyletic Basal Acoelomorpha". Molecular Biology and Evolution26 (10): 2397–2406. doi:10.1093/molbev/msp150. PMID19602542.Cite uses deprecated parameters (help)
^Helfenbein, Kevin G.; Fourcade, H. Matthew; Vanjani, Rohit G.; Boore, Jeffrey L. (2004). "The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister group to protostomes". Proceedings of the National Academy of Sciences of the United States of America101 (29): 10639–10643.
^Papillon, Daniel; Perez, Yvan; Caubit, Xavier; Yannick Le, Parco (2004). "Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome". Molecular Biology and Evolution21 (11): 2122–2129.
^Nielsen, C. 2001. Animal Evolution: Interrelationships of the Living Phyla. Second Edition. Oxford University Press, Oxford.