We follow, with some modification, the higher classification of turtles proposed by Gaffney (1984). In his taxonomic scheme, living turtles belong to the gigaorder Casichelydia, and either the megaorder Pleurodira (side-necked turtles, see below) or the megaorder Cryptodira (hidden-necked turtles, see below). There are 13 living families and 289 living species. See Hunt (1958) for a discussion of the proper ordinal name for turtles.

The oldest fossil turtles have been found in the Triassic deposits of Germany. These fossils have been assigned to the genus Proganochelys (= Triassochelys), which, along with the fossil genera Proterocheris, Saurischiocomes, and Chelytherium, belong to the gigaorder Proganochelydia (Romer, 1956; Gaffney, 1975b). Only some skeletal features of these are known completely. The skull is solidly roofed, with the external parts sculptured. The postfrontal, lacrimal, and supratemporal are (or may be) present, and the external nares are divided by a bony bar. The quadrate lacks the strong curvature around the stapes that is characteristic of most turtles. There are small teeth on bones of the palate and rudimentary teeth on the jaw margins. Proganochelydians have seven cervicals—the 8th vertebra is a dorsal rather than a cervical, its arch fused to the nuchal—and the cervicals are amphicoelous, with two-headed ribs. The bones of the pectoral girdle, although partially fused with the plastron, can still be identified individually as clavicle, interclavicle, and cleithrum. The pelvis probably was more or less firmly attached, even sometimes fused, to the plastron. The peripherals of the carapace apparently were very numerous; the neurals are long and narrow; and there are nine costals. The plastron contains several extra bones, in the form of two pairs of mesoplastra, which are absent in most modern turtles. The buttress elements of the plastron do not reach the carapacial costals. There are dermal tubercles on the neck and tail, and presumably the head and limbs could not be pulled into the shell. Likely these primitive turtles were amphibious (Romer, 1956).

All other turtles are assigned to the gigaorder Casichelydia. Gaffney (1975b, 1984) compared the skulls of proganochelydians and casichelydians, and found the floor of the middle ear (acoustic-jugular cavity) and the interpterygoid vacuity to be open in proganochelydians but closed in casichelydians. The quadrate does not form the lateral wall of the middle ear in proganochelydians, but does so in casichelydians, and the following features are present in Proganochelydia but not in Casichelydia: a bladelike (cultiform) process on the parasphenoid, palatal teeth, a well-developed median tubercle on the basioccipital, and the external opening of the nostrils divided by a dorsal premaxillary process. In contrast, casichelydians have both an expanded supraoccipital crista and an antrum postoticum which are absent in proganochelydians. The Casichelydia became dominant during the Jurassic and remained so ever since. They were mainly amphibious, but some species have become marine (Cheloniidae, Dermochelyidae) or terrestrial (Emydidae, Testudinidae). Two modern megaorders of turtles have arisen from early casichelydians in the Triassic and Jurassic: the Pleurodira and the Cryptodira. The Cryptodira continued as the main evolutionary line of turtles, with the Pleurodira appearing as an aberrant but structurally conservative side branch. The basic skull character differentiating these two turtle groups is that the jaw adductor tendon passes over the trochlear-oticum process in cryptodires, but passes over the trochlear-pterygoid process in pleurodires (Gaffney, 1979b). The following media clip compares the Cryptodira and Pleurodira (Pleurodiran/cryptodiran turtles; modified from Romer, 1956, and Gaffney, 1975b).

The earliest cryptodiran fossil, Kayentachelys aprix, is from the Lower (Early) Jurassic (Gaffney et al., 1987). By the Early Cretaceous they had become the dominant turtles of northern regions, and some species had invaded the oceans. Their heads can be withdrawn in a vertical flexure, because the cervical vertebrae can be bent into a sigmoid curve. The Cryptodira is considered to be the more advanced group of turtles. According to Gaffney (1984) the cryptodiran line is composed of two subdivisions called hyperorders. The extinct hyperorder Pleurosternoidea is comprised of the family Pleurosternidae (= Glyptopsidae, Jurassic). The second hyperorder, Daiocryptodira, includes the parvorder Baenoidea (family Baenidae, Cretaceous-Eocene), and the parvorder Eucryptodira, which includes living cryptodirans. Pleurosternids and baenoids retain several primitive characters. They retain nasal bones and thus have the prefrontals separated and not in contact at the midline of the skull. The foramen for the internal posterior cortical canal lies midway along the length of the basisphenoid-pterygoid suture. They also have a well-developed stapedial artery and reduced orbital and palatine arteries. The neck vertebrae lacked mechanisms to retract the head, and no formed central articulations were present in the early species. Mesoplastral bones and paired intergular scutes were also present. The parvorder Eucryptodira is composed of several superfamilies: the Trionychoidea (Cretaceous-Recent), including the living families Kinosternidae, Dermatemydidae, Carettochelyidae, and Trionychidae; the marine Chelonioidea (Jurassic-Recent), including the extinct families Plesiochelyidae (Jurassic), Protostegidae (Cretaceous), and Toxochelyidae (Cretaceous-Eocene) and the living families Cheloniidae and Dermochelyidae; the Testudinoidea (Paleocene-Recent), including the living families Chelydridae, Platysternidae, Emydidae, and Testudinidae. Gaffney (1984) places the Chelydridae in the separate infraorder Chelydroidea.

The Pleurodira are considered by many experts to be more primitive than the Cryptodira. Surprisingly, these turtles appear in the fossil record an entire period (about 50 million years) later than the cryptodirans: the earliest known pleurodiran fossils are Notoemys laticentralis and Platychelys oberndorfi from the Late Jurassic. The pleurodirans withdraw their necks laterally; that is, they bend the neck sideways to tuck the head under the rim of the shell. This has given rise to their common name: side-necked turtles. Two living families are included, Pelomedusidae and Chelidae, and the extinct family Araripemydidae.