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Cynodonts have nearly all the characteristics of mammals. Their teeth were fully differentiated, the braincase bulged at the back of the head, and many of them walked in an upright manner. Cynodonts still laid eggs, as all Mesozoic proto-mammals probably did. Their temporal fenestrae were much larger than in its ancestors, and the widening of the zygomatic arch allowed for more robust jaw musculature supporting the evidence of a more mammal-like skull. They also have the secondary palate that other primitive therapsids lacked, except the therocephalians, who were the closest relatives of cynodonts. Their dentary was the largest bone in their lower jaw, as other smaller bones moved into the ears. They were probably warm-blooded, and covered in hair.
The cynodonts themselves are part of a group of therapsids called theriodonts, together with the extinct gorgonopsians and the therocephalians. Cynodonts evolved shortly before the end of Permian. The oldest and the most basal cynodont yet found is Charassognathus. Other basal cynodonts were the Procynosuchids, a family that includes Procynosuchus and Dvinia. Cynodonts were among the few groups of synapsids that survived the Permian–Triassic extinction event and had a slow recovery after the extinction.
The most derived cynodonts are found within the clade Eucynodontia, which also contains the members of Mammalia. Representative genera include the large carnivorous cynognathids, equally large herbivorous traversodonts, and small and mammal-like tritylodontids and ictidosaurs. It is likely that cynodonts were at least partially if not completely warm-blooded, covered with hair, which would have insulated them and helped to maintain a high body temperature. The mammal-like structure of cynodonts hints that all mammals have descended from a single group of eucynodonts.