The goal of the Quagga project is to breed animals “indistinguishable” from quaggas, but this is impossible as selection has been solely for coat coloration. Genetic and morphological differences exist between quaggas and other plains zebras so that in the absence of selection for these characteristics it is untenable to refer to the rebred animals as "quaggas." Even so, these animals introduced into habitats once occupied by quaggas will aid in their rewilding. The relationship between the Quagga Project and conservation is discussed from the perspective of whether funds used for rebreeding could have been more fruitfully expended to conserve endangered organisms and threatened habitats in South Africa. Nonetheless, the Quagga project has been successful in inspiring support from a variety of people and organizations; as such, it could serve as a model for conservation ventures. The challenges facing wild equines are discussed with reference to Grévy's zebras and Selous’s zebras, especially climate change, habitat loss, and hunting.

Reinhold Rau of the South Africa Museum in Cape Town felt a moral duty to rebreed quaggas. Sequencing showed that mitochondrial DNA from quaggas was identical, or almost so, with corresponding sequences from plains zebras. This conclusion provided the rationale for rebreeding but wildlife officials refused funding. Instead, supported by many people and organizations, Rau and others initiated the Quagga Project which selected offspring from a founder population of nineteen plains zebras with brown coloration of their bodies and relatively few stripes on their legs and hindquarters. By the fourth and fifth generation, animals with coat coloration resembling that of quaggas have been selectively bred, and those with the best coat coloration are named “Rau Quaggas.” Rau Quaggas and other Quagga Project zebras are present in national parks, on private land, and as the Core Herd of the Quagga Project at four locations. Rebreeding of quaggas is compared with other de-extinction projects such as the Giant Tortoise Restoration Initiative that aims to rebreed an extinct species of Galapagos tortoise whose genes are present in an extant tortoise population.