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Background and purpose: Misuse of antibiotics diminishes microbial balance of the body which has led to emergence of new diseases. In this research, we studied the effect of essential oils of Zingiber officinale, Cinnamomum verum, Trachyspermum ammi, and Carum carvi on intestinal microorganisms’ effect in dysbiosis in vitro. Materials and methods: Essential oils were prepared by indirect steam distillation. Pure and lyophilized microorganisms were purchased from Iranian Research Organization for Science and Technology (IROST). After the culture media was preapered the wells were created over the agar plates and antimicrobial activity was defined by measuring the inhibition zone diameter after 24 hours. Antibacterial effects of the essential oils were studied by well assay methods, Minimum Inhibitory Concentration (MIC), and Minimum Bactericidal Concentration (MBC). Results were interpreted using CLSI standards. Results: Cinnamomum verum had the highest inhibitory effect on all pathogens. Trachyspermum ammi essential oils had moderate inhibitory effect on all pathogens except shigella Flexneri. The essential oils of Cuminum cyminum and Carum carvi had similar inhibitory effects. Ginger essential oil showed no inhibitory effect on any of the pathogens. Conclusion: The highest inhibitory effect on pathogens was seen in Trachyspermum ammi essential oil, while it had the least inhibitory effect on beneficial microorganisms. Cinnamomum verum essence, with very good inhibitory effect on pathogens and inhibition of some useful microorganisms, can be promising to make effective drug by modulating the activity of pathogens effective in dysbiosis of the clone.