While the project is progressing well, there are still those who have certain reservations or are outright against the project.

The genetic basis of the Quagga Breeding Project, relies on the demonstration by Higuchi et al (1987) (Mitochondrial DNA of the Extinct Quagga: Relatedness and Extent of Postmortem Change. Journel of Molecular Evolution 25:283-287) that the mitochondrial DNA of the Quagga is identical to that of other Plains Zebras. Therefore the Quagga and other Plains Zebras belong to the same species and consequently the Quagga should be considered merely a different population (or deme), of the Plains Zebra.

It has been argued that there might have been other non-morphological, genetically-coded features (such as habitat adaptations) unique to the Quagga and that therefore, any animal produced by a selective breeding programme would not be a genuine Quagga. Since there is no direct evidence for such characters and since it would be impossible now to demonstrate such characters were they to exist, this argument has limited value. The definition of the Quagga can only rest on its well-described morphological characteristics and, if an animal is obtained that possesses these characters, then it is fair to claim that it is a representation of, at least, the visible Quagga phenotype.