Microorganisms play an extensive role in the decomposition of many organic matters and are in symbiotic relationship with plants and animals. In this study, concentration containing 57 mg/ml malathion was diluted and used to spray soil sample collected from Riyadh area, Saudi Arabia Total chromosomal soil microorganisms were isolated from sprayed and non sprayed samples. Absence and presences of PCR band profiles were assumed to represent the absence or presence of bacteria. A maximum 7mg/ml and minimum 0.2mg/4.16 ul of malathion concentration was used in a nutrient agar medium for bacterial growth. The fingerprinting profiles of treated soil samples demonstrated the missing of some fingerprint bands which were present in the profiles of non treated soil samples. It was concluded that malathion had a misbalancing effect on the soil flora bacteria. However, smearing with maximum malathion concentration in nutrient agar supporting bacterial growth was observed. While a minimum concentration in the same nutrient agar was not supporting.