A study was conducted on 16S rRNA sequences for Klebsiella aerogenes, K. pneumoniae, and Proteus mirabilis strains from Saudi soil to investigate the genetic variations among them. The analysis revealed minimal differences among these strains. Single nucleotide polymorphisms (SNPs) were identified in the 16S rRNA genes of K. aerogenes and K. pneumoniae strains, indicating genetic diversity within these bacterial populations that could potentially influence their phenotypic traits. Additionally, the presence of insertions and deletions (indels) in comparison to separate rRNA gene sequences suggested structural variations in the genetic makeup of these strains. Electropherograms displayed multiple peaks at specific nucleotide positions, indicating the presence of different nucleotides within the gene copies. This suggests the existence of genetic heterogeneity within the populations, possibly due to the coexistence of multiple variants of the 16S rRNA gene within individual bacterial strains. Overall, there are valuable insights into the genetic variations and relationships among these bacterial strains found in Saudi soil. Understanding the genetic diversity of these bacterial strains is crucial for comprehending evolutionary relationships and potential differences in phenotypic characteristics. The results contribute to the knowledge about the genetic variation of bacteria in soil in Saudi Arabia, with potential implications for environmental microbiology and biotechnology.