Although the maned wolf displays many fox-like characteristics, it is not closely related to foxes and lacks the elliptical pupils found in foxes. The maned wolf's evolutionary relationship to the other members of the canid family makes it a unique animal. Electrophoretic studies did not link Chrysocyon with any of the other canids studied. One conclusion of this study is that the maned wolf is the only survivor of the late Pleistocene extinction of the large South American canids. Fossils of the maned wolf from the Holocene and the late Pleistocene have been excavated from the Brazilian Highlands.
A study, published in 2003, on the brain anatomy of several canids, placed the maned wolf together with the Falkland Islands wolf, and with pseudo-foxes of the genus Pseudalopex. One study based on DNA evidence, published in 2009, showed that the extinct Falkland Islands wolf was the most closely related species to the maned wolf in historical times, and shared a common ancestor with it about 6 million years ago. Its closest living relative is the bush dog (genus Speothos), with a more distant relationship to other South American canines (the short-eared dog, the crab-eating fox and the 'false foxes' or Pseudalopex).
The maned wolf is not closely related to any other living canid. It is not a fox, wolf, coyote, dog, or jackal, but a distinct canid, although previously it had been placed in Canis and Vulpes genera based on morphological similarities.