Soil bacteria play an essential function in different biogeochemical cycles. The present study aimed to estimate microbial diversity in five natural environments of Saudi Arabia by isolating and identifying thermophiles and thermo-tolerant bacteria. The collected soil samples were analyzed physically, chemically, and microbiologically. Biochemical and molecular techniques identified many bacteria, including Enterobacter ludwigii, Enterobacter sp., Enterobacteriaceae bacterium, Bacillus sp., Bacillus subtilis, Bacillus licheniformis, Paenibacillus sp., Paenibacillusdendritiformis, Paenibacillus lactis, Pseudomonas aeruginosa, Pseudoalteromonas sp., Staphylococcus sp., and Brevibacillus borstelensis. This is the first report of the Enterobacter ludwigii isolate from the soil samples collected in Saudi Arabia to the best of the authors' knowledge, which is part of plant growth-promoting rhizobacteria (PGPR) can influence the composition of the rhizosphere soils, root tissues, and enhanced plant outgrowth. The presence of these bacteria could be utilized to promote agricultural practices in the deserts in Saudi Arabia.