Background: Pseudomonas aeruginosa is an opportunistic pathogen which causes a range of infections. Satureja khuzestanica essences have antibacterial effect. Aim: This study aimed to investigate the inhibitory effects of S. khuzestanica essential oil against housekeeping fabD and exo A genes of Pseudomonas aeruginosa from hospital isolates using RT-PCR technique. Material and Methods: The inhibition effect was conducted according to the CLSI 2013 standards and instructions. The minimum inhibitory concentration (MIC) of essence was determined according to CLSI. Isolates were collected of burn patients in the Motahari hospital, Tehran and cultured on proper media and confirmed using microbiology and biochemical. Susceptibility and MIC of S. khuzestanica were determined against P. aeruginosa. Expressions of exoA and Housekeeping fabD genes were evaluated using RT-PCR in presence and lack tests of S. khuzestanica essence. Results: Diameter of inhibition zone of S. khuzestanica essence against P. aeruginosa was 25 mm. MIC of essence was 0.31 μl/ml. Gene expression of exo A under inducing with essential oil of S. khuzestanica reduced but gene expression of housekeeping gene DNA gyraseA not changed before and after exposure. Conclusion: Our results showed that S. Khuzestanica could cause reduction in drug resistance and inhibition of gene expression of exoA in P. aeruginosa. Also, RTPCR is an effective technique for evaluation of gene expression.