The desert tortoise is one of four allopatric North American tortoises. It occurs in the Mojave and Sonoran deserts of the southwestern United States and Mexico.

Auffenberg (1976) divided the genus Gopherus (consisting of four species, G. agassizi, G. berlandieri, G.flavomarginatus, and G. polyphemus) in two osteological groups. Bramble (1982), using morphological and palaeontological data, divided the genus Gopherus into two separate complexes, each with two species. He established a new genus, Scaptochelys, for agassizi and berlandieri, retaining Gopherus for polyphemus and flavomarginatus. Bour and Dubois (1984) noted that Xerobates Agassiz had priority over Scaptochelys Bramble. Using mitochondrial DNA (mtDNA), Lamb et al. (1989) evaluated the evolutionary relationships of the North American tortoises, particularly the desert tortoise. They concluded that the mtDNA analysis provides strong support for generic recognition of the two distinct species groups described by Bramble (1982).

Until a few decades ago, the desert tortoise was widespread at lower elevations throughout the Mojave and Sonoran deserts of the U.S.A. In the northern and western parts of the geographic range, large and relatively homogeneous populations with densities exceeding 1,000/sq km extended throughout parts of California, and probably into Nevada and Utah. In terms of biomass, the tortoise played an important role in the ecosystems. In most areas, numbers have declined dramatically and the extent of populations has been reduced. Most populations are now isolated and low in numbers. Conservation of the desert tortoise is a highly visible and political issue in the U.S.A., but not in Mexico.