Bolson Tortoises (Gopherus flavomarginatus) are a keystone species whose burrows are a unique microhabitat for a large number of vertebrates in the Chihuahuan Desert. Through the construction of burrows, Bolson Tortoises modify the habitat, resulting in greater structural complexity. This in turn results in a greater number of niches and therefore in greater biodiversity, providing not only shelter from predators, adverse climatic conditions, and fires, but ideal conditions for reproduction, socialization and feeding of various species. The potential distribution of Bolson Tortoises, eight mammal, four bird, and seven reptile species that use Bolson Tortoise burrows was modeled for the present, as well as for 2050 and 2070. The maximum entropy model (Maxent) included 19 bioclimatic layers and altitude. The models suggest a decrease in the potential distribution of G. flavomarginatus (its distribution was reduced by 85.95% from the present scenario to 2070) and 17 out of the 19 species of vertebrates that use their burrows, in both projected scenarios. This indicates climate change would negatively affect not only species with restricted or micro-endemic distributions, such as Bolson Tortoises, but also those of wide distribution, such as Coyotes (Canis latrans), Striped Skunks (Mephitis mephitis), and Scaled Quail (Callipepla squamata). The models also indicate that the percentage of geographical overlap of ≥12 of vertebrate species with G. flavomarginatus will decrease drastically by 2070, thereby reducing the availability of microhabitat (G. flavomarginatus burrows) for these species. Reduced availability of microhabitats could affect the ability of these accompanying vertebrates to hide from predators or adverse weather conditions, as well as to find sites for reproduction or feeding (Lepus californicus, Athene cunicularia, M. mephitis, C. latrans, Lynx rufus, Vulpes macrotis, and M. mephitis). Our work emphasizes the importance of conservation actions to help Bolson Tortoises (G. flavomarginatus), which in turn will benefit other species of mammals, birds, and reptiles that require the presence of tortoise burrows as microhabitats.