All chordates possess, at some point during their larval or adult stages, five distinctive physical characteristics (synapomorphies) that distinguish them from other taxa.

These five synapomorphies are a notochord, a hollow dorsal nerve cord, an endostyle or thyroid, pharyngeal slits, and a post-anal tail.

Chordates are divided into three subphyla: Vertebrata (fish, amphibians, reptiles, birds and mammals), whose notochords are replaced by a cartilaginous/bony axial endoskeleton (spine) and are cladistically and phylogenetically a subgroup of the clade Craniata (i.e. chordates with a skull); Tunicata or Urochordata (sea squirts, salps, and larvaceans), which only retain the synapomorphies during their larval stage; and Cephalochordata (lancelets), which resemble jawless fish but have no gills or a distinct head.

Cephalochordates, one of the three subdivisions of chordates, are small, "vaguely fish-shaped" animals that lack brains, clearly defined heads and specialized sense organs.

[29] The other two groups, the sea squirts and the salps, metamorphize into adult forms which lose the notochord, nerve cord, and post anal tail.

The salps float in mid-water, feeding on plankton, and have a two-generation cycle in which one generation is solitary and the next forms chain-like colonies.

[9] All of the earliest chordate fossils have been found in the Early Cambrian Chengjiang fauna, and include two species that are regarded as fish, which implies that they are vertebrates.

Because the fossil record of early chordates is poor, only molecular phylogenetics offers a reasonable prospect of dating their emergence.

[43] Three enigmatic species that are possible very early tunicates, and therefore deuterostomes, were also found from the Ediacaran period – Ausia fenestrata from the Nama Group of Namibia, the sac-like Yarnemia ascidiformis, and one from a second new Ausia-like genus from the Onega Peninsula of northern Russia, Burykhia hunti.

[46][47] Ausia and Burykhia lived in shallow coastal waters slightly more than 555 to 548 million years ago, and are believed to be the oldest evidence of the chordate lineage of metazoans.

Fossils of one major deuterostome group, the echinoderms (whose modern members include starfish, sea urchins and crinoids), are quite common from the start of the Cambrian, 542 million years ago.

[54] The best known and earliest unequivocally identified Tunicate is Shankouclava shankouense from the Lower Cambrian Maotianshan Shale at Shankou village, Anning, near Kunming (South China).

[14] Combining such analyses with data from a small set of ribosome RNA genes eliminated some older ideas, but opened up the possibility that tunicates (urochordates) are "basal deuterostomes", surviving members of the group from which echinoderms, hemichordates and chordates evolved.

[14][57] Since early chordates have left a poor fossil record, attempts have been made to calculate the key dates in their evolution by molecular phylogenetics techniques—by analyzing biochemical differences, mainly in RNA.

[60][61][62][63][64] Cephalochordata (lancelets) Appendicularia (larvaceans) Thaliacea Phlebobranchia Aplousobranchia Stolidobranchia Myllokunmingiida † Anaspidomorphi † Conodonta † Myxini (hagfish) Hyperoartia (lampreys) Pteraspidomorphi † Thelodonti † Galeaspida † Pituriaspida † Osteostraci † "Placodermi" † (paraphyletic) "Acanthodii" † (paraphyletic) Holocephali Selachimorpha (sharks) Batoidea (rays) Cladistia Chondrostei Holostei Teleostei Actinistia (coelacanths) Dipnoi (lungfish) Amphibia Sauropsida Synapsida The closest relatives of the chordates are believed to be the hemichordates and Echinodermata, which together form the Ambulacraria.

Hemichordates ("half chordates") have some features similar to those of chordates: branchial openings that open into the pharynx and look rather like gill slits; stomochords, similar in composition to notochords, but running in a circle round the "collar", which is ahead of the mouth; and a dorsal nerve cord—but also a smaller ventral nerve cord.

The extinct graptolites, colonial animals whose fossils look like tiny hacksaw blades, lived in tubes similar to those of pterobranchs.

[65] Echinoderms differ from chordates and their other relatives in three conspicuous ways: they possess bilateral symmetry only as larvae – in adulthood they have radial symmetry, meaning that their body pattern is shaped like a wheel; they have tube feet; and their bodies are supported by dermal skeletons made of calcite, a material not used by chordates.

The feet are powered by another unique feature of echinoderms, a water vascular system of canals that also functions as a "lung" and surrounded by muscles that act as pumps.

Crinoids are typically sessile and look rather like flowers (hence the common name "sea lilies"), and use their feather-like arms to filter food particles out of the water; most live anchored to rocks, but a few species can move very slowly.