A knowledge gap exists regarding the potential of thermophilic bacteria in the hot springs in Saudi Arabia as a resource for medically useful compounds. This study aimed to investigate the microbial diversity in the soils of hot springs at three locations on the west coast of Saudi Arabia, including Jizan, Al Lith, and Tabuk. Soil samples were extracted for rDNA 16S, and the results were analysed for microbial diversity and abundance. The results showed the dominance of Acidobacteriota, Actinobacteriota, Desulfobacterota, Firmicutes, Halanaerobiaeota, Nitrospirota, and Thermotogota. Actinobacteriota dominated the microbial population in Al Lith soil, while Deinococcota were dominant in Jizan soil and Chloroflexi in Tabuk soil. Firmicutes and Proteobacteria had high microbial populations in all three soils. Based on principal coordinate analysis, the normalized relative microbial diversity of all soils showed differences as well as similarities in the distribution of taxonomic classifications between soil samples. In conclusion, the microbial diversity in Jizan, Al Lith, and Tabuk included a variety of microorganism species that can potentially be used in biotechnology as a novel source for industrial production of medically useful compounds.