Due to the applied rules by various pollution control authorities to maintain the discharged norms of wastes to treated water, the food business has a difficult challenge. The wastewater contains high levels of fats, grease, and oils increased every year. So, this work was devoted to isolating and investigating microorganisms that could be used to treat wastewater as an alternative to chemical treatment. Seven Bacilli were locally isolated from soil and tested for lipase production. The AMG-Kh-B2 was the most potent isolate that produced the highest lipase activity (36.4 U.mL-1) after 3 days of fermentation. The Bacillus isolate (AMG-Kh-B2) was identified as Bacillus licheniformis through the BLAST analysis of the amplified 16S ribosomal RNA gene sequence. Mutation induced by ethyl methanesulfonate (EMS) was performed to improve lipase enzyme production. The mutant M-9 was the highest enzyme producer since it produced 262.64 % lipase enzyme higher than the wild-type strain (WT). The use of the random amplified polymorphic DNA (RAPD) approach using polymerase chain reaction (PCR) on certain excellent mutants resulted in a correlation between the genetic characteristics of the excellent mutants (M-9 and M-27) and the genetic characteristics of the wild type strain (WT). The evidence of genetic diversity created in B. licheniformis DNA following EMS-mutagenesis was corroborated by differences in RAPD patterns. As a result, cluster analysis was utilized to classify the strains under analysis into clusters that potentially recognize the genetic variety of lipase-producing mutants.