The Desert Tortoise derives its common name from its habitat in the arid deserts of southwestern North America. The term "desert tortoise" accurately describes both habitat and lifestyle, distinguishing them from forest, grassland, or aquatic turtles. This name is universally recognized and applies to two closely related species now recognized as distinct: the Mojave Desert Tortoise (Gopherus agassizii) and the Sonoran Desert Tortoise (Gopherus morafkai). For many decades, these were considered a single species, but genetic and morphological analysis published in 2011 recognized them as distinct species separated by the Colorado River. The Mojave Desert Tortoise occurs west and north of the Colorado River in California, Nevada, southwestern Utah, and northwestern Arizona. The Sonoran Desert Tortoise occurs east and south of the Colorado River in Arizona and Sonora, Mexico.
Alternate common names distinguish the two species when specificity is needed. "Mojave Desert Tortoise" or "Agassiz's Desert Tortoise" refers specifically to Gopherus agassizii, while "Sonoran Desert Tortoise" or "Morafka's Desert Tortoise" refers to Gopherus morafkai. When the distinction is not emphasized, simply "Desert Tortoise" typically refers to both species collectively, as their care requirements and ecology are similar. Regional names may reference specific geographic areas within their ranges. Historical literature uses "desert tortoise" without distinction, as the split into two species is relatively recent.
Scientifically, Desert Tortoises belong to the genus Gopherus, family Testudinidae, which includes all tortoises. The genus Gopherus contains four or five recognized species (depending on taxonomic authority) of North American gopher tortoises, all characterized by adaptations for digging including flattened, shovel-like front legs and domed shells. The genus name Gopherus references their burrowing behavior, likening them to gophers in their excavation of underground refugia. The specific epithet "agassizii" honors Swiss-American naturalist Louis Agassiz, while "morafkai" honors turtle biologist David Morafka who studied desert tortoises extensively.
The Mojave Desert Tortoise (G. agassizii) was described by Cooper in 1861. The Sonoran Desert Tortoise (G. morafkai) was recognized as a distinct species by Murphy et al. in 2011, separated from agassizii based on genetic, morphological, and geographic evidence. Prior to 2011, all desert tortoises were considered subspecies or populations of G. agassizii. The recognition of two species has important conservation implications, as each has distinct status, threats, and management needs. The Mojave Desert Tortoise is federally listed as Threatened under the U.S. Endangered Species Act, while the Sonoran Desert Tortoise has different conservation status.

