Essential oils are potential antimicrobial agents and can be used as active ingredients in the pharmaceutical, food and cosmetics industries. This work intends to evaluate the antibacterial activity and design a strategy for the proposition of the mechanism of action of Melaleuca leucadendra essential oil. Optimum concentration of the bacteria and the phase where they had the highest pathogenic activity were determined. Results show that for each microorganism it is necessary to use a different concentration at the time of adjusting the initial inoculum, and that the time to achieve exponential growth phase varies from one to the other. M. leucadendra essential oil demonstrated in vitro antimicrobial properties. This oil was chemically characterized and the main compounds were evaluated by their mechanism of antibacterial action based on structure-activity analysis. The mechanism is related to the increase of bacteria cell membrane permeability. This indication was confirmed by flow cytometry and transmission electronic microscopy. Thus, in silico analysis is an important tool in the search for new antimicrobial agents and these results showed that M. leucadendra essential oil may be useful on the development of new chemotherapies or food preservation systems.