The quagga was the first extinct animal to have its DNA analysed, and this 1984 study launched the field of ancient DNA analysis.
It confirmed that the quagga was more closely related to zebras than to horses, with the quagga and mountain zebra (Equus zebra) sharing an ancestor 3–4 million years ago.
An immunological study published the following year found the quagga to be closest to the plains zebra.
A 1987 study suggested that the mtDNA of the quagga diverged at a range of roughly 2% per million years, similar to other mammal species, and again confirmed the close relation to the plains zebra.

Later morphological studies came to conflicting conclusions.
A 1999 analysis of cranial measurements found that the quagga was as different from the plains zebra as the latter is from the mountain zebra.
A 2004 study of skins and skulls instead suggested that the quagga was not a distinct species, but a subspecies of the plains zebra.
In spite of these findings, many authors subsequently kept the plains zebra and the quagga as separate species.

A genetic study published in 2005 confirmed the subspecific status of the quagga.
It showed that the quagga had little genetic diversity, and that it diverged from the other plains zebra subspecies only between 120,000 and 290,000 years ago, during the Pleistocene, and possibly the penultimate glacial maximum.
Its distinct coat pattern perhaps evolved rapidly because of geographical isolation and/or adaptation to a drier environment.
In addition, plains zebra subspecies tend to have less striping the further south they live, and the quagga was the most southern-living of them all.
Other large African ungulates diverged into separate species and subspecies during this period, as well, probably because of the same climate shift.

The simplified cladogram below is based on the 2005 analysis (some taxa shared haplotypes and could, therefore, not be differentiated):
A 2018 genetic study of plains zebras populations confirmed the quagga as a member of the species.
They found no evidence for subspecific differentiation based on morphological differences between southern populations of zebras, including the quagga.
Modern plains zebra populations may have originated from southern Africa, and the quagga appears to be less divergent from neighbouring populations than the northernmost living population in northeastern Uganda.
Instead, the study supported a north–south genetic continuum for plains zebras, with the Ugandan population being the most distinct.
Zebras from Namibia appear to be the closest genetically to the quagga.
The quagga was the first extinct animal to have its DNA analysed, and this 1984 study launched the field of ancient DNA analysis. It confirmed that the quagga was more closely related to zebras than to horses, with the quagga and mountain zebra (Equus zebra) sharing an ancestor 3–4 million years ago. An immunological study published the following year found the quagga to be closest to the plains zebra. A 1987 study suggested that the mtDNA of the quagga diverged at a range of roughly 2% per million years, similar to other mammal species, and again confirmed the close relation to the plains zebra.
Later morphological studies came to conflicting conclusions. A 1999 analysis of cranial measurements found that the quagga was as different from the plains zebra as the latter is from the mountain zebra. A 2004 study of skins and skulls instead suggested that the quagga was not a distinct species, but a subspecies of the plains zebra. In spite of these findings, many authors subsequently kept the plains zebra and the quagga as separate species.
A genetic study published in 2005 confirmed the subspecific status of the quagga. It showed that the quagga had little genetic diversity, and that it diverged from the other plains zebra subspecies only between 120,000 and 290,000 years ago, during the Pleistocene, and possibly the penultimate glacial maximum. Its distinct coat pattern perhaps evolved rapidly because of geographical isolation and/or adaptation to a drier environment. In addition, plains zebra subspecies tend to have less striping the further south they live, and the quagga was the most southern-living of them all. Other large African ungulates diverged into separate species and subspecies during this period, as well, probably because of the same climate shift.
The simplified cladogram below is based on the 2005 analysis (some taxa shared haplotypes and could, therefore, not be differentiated):
A 2018 genetic study of plains zebras populations confirmed the quagga as a member of the species. They found no evidence for subspecific differentiation based on morphological differences between southern populations of zebras, including the quagga. Modern plains zebra populations may have originated from southern Africa, and the quagga appears to be less divergent from neighbouring populations than the northernmost living population in northeastern Uganda. Instead, the study supported a north–south genetic continuum for plains zebras, with the Ugandan population being the most distinct. Zebras from Namibia appear to be the closest genetically to the quagga.
Quagga