There is a dispute among biologists as to how to properly classify the various species of zebra. It is thought that the plains zebra and mountain zebra belong to the subgenus Hippotigris and that Grévy's zebra is the sole species of subgenus Dolichohippus. This is on account of Grévy's zebra resembling an ass (subgenus Asinus), while the plains zebra and mountain zebra are more horse-like. All three animals belong to the genus Equus along with other living equids. However, recent phylogenetic evidence finds that plains zebras are more closely related to Grévy's zebras than mountain zebras. In areas where plains zebras are sympatric with Grévy's zebras, it is not unusual to find them in the same herds and fertile hybrids occur. In captivity, plains zebras have been crossed with mountain zebras. The hybrid foals lacked a dewlap and resembled the plains zebra apart from their larger ears and their hindquarters pattern.
In 2004, C. P. Groves and C. H. Bell investigated the taxonomy of the zebra genus, Equus, subgenus Hippotigris. They published their research in the journal Mammalian Biology. They revised the subspecies of the plains zebra Equus quagga. Six subspecies are now recognisable.
- Quagga, †Equus quagga quagga – Boddaert, 1785
- Burchell's zebra, Equus quagga burchellii – Gray, 1824
- Grant's zebra, Equus quagga boehmi – Matschie, 1892
- Maneless zebra Equus quagga borensis – Lönnberg, 1921
- Chapman's zebra, Equus quagga chapmani – Layard, 1865
- Crawshay's zebra, Equus quagga crawshayi – De Winton, 1896
Sometimes another subspecies is distinguished in Eastern Zimbabwe and Western Mozambique:
The quagga was originally classified as a separate species, Equus quagga, in 1778. Over the next 50 years or so, many other zebras were described by naturalists and explorers. Because of the great variation in coat patterns (no two zebras are alike), taxonomists were left with a great number of described "species", and no easy way to tell which of these were true species, which were subspecies, and which were simply natural variants. The quagga was the first extinct creature to have its DNA studied. Recent genetic research at the Smithsonian Institution has demonstrated that the quagga was in fact not a separate species at all, but diverged from the plains zebra, between 120,000 and 290,000 years ago, and suggests that it should be named Equus burchellii quagga. However, according to the rules of biological nomenclature, where there are two or more alternative names for a single species, the name first used takes priority. As the quagga was described about 30 years earlier than the Burchell's zebra, it appears that the correct terms are E. quagga quagga for the quagga and E. quagga burchellii for the plains zebra, unless "Equus burchellii" is officially declared to be a nomen conservandum.
Burchell's zebra was thought to have been hunted to extinction. However, Groves and Bell concluded in their 2004 publication that "the extinct true Burchell's zebra" is a phantom. Careful study of the original zebra populations in Zululand and Swaziland, and of skins harvested on game farms in Zululand and Natal, has revealed that a certain small proportion shows similarity to what now is regarded as typical "burchellii". The type localities of the subspecies Equus quagga burchellii and Equus quagga antiquorum (the Damara zebra) are so close to each other that the two are in fact one, and that therefore the older of the two names should take precedence over the younger. They therefore say that the correct name for the southernmost subspecies must be burchellii not antiquorum. The subspecies Equus quagga burchellii still exists in KwaZulu-Natal and in Etosha.
A 2018 DNA study found no evidence for a subspecies structure, but instead observed a north-south genetic continuum, with plains zebra in Uganda (the most northern population) the most distinct.