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A unique relictual population of Fouquieria columnaris is located in Sonora, along a 45-km strip of land encompassing Punta Cirio in the Sonoran Desert. The interaction of plants with microorganisms is an important adaptation to survival in desertic areas. The present study reports the abundance of bacteria, actinohacteria, and filamentous and arbuscular mycorrhizal fungi (AMF) in the rhizosphere of F. columnaris at Punta Cirio. Also, the genetic variability of F. columnaris was analyzed using amplied fragment length polymorphism markers. Bacteria and fungi in 27 soil samples from the rhizosphere of F. columnaris at 3 hills with low, medium, and high elevations were analyzed. The total bacterial, actinobacterial, and filamentous fungal counts did not differ among sites or elevations; no interaction between site and elevation was found. Nitrogen-fixing bacteria varied according to site but not elevation, whereas phosphorus-solubilizing bacteria were undetected. Filamentous fungi were dominated by Aspergillus spp. (48%) and Penicillium spp. (28%), which together represented 76% of the total average colony-forming units. The spore density of AMF ranged from 109 to 245 per 100 g of soil, and 65 to 80% of roots were colonized by hyphae, vesicles, or arbuscles of AMF. The DNA analysis generated an average similarity coefficient of 0.89, which could indicate high genetic homogeneity within the evaluated F. columnaris population.