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The paper presents the results of experimental studies of molecular destruction in gaseous and liquid medium using microwave discharge plasma at atmospheric pressure. As the gas medium hydrocarbon gas is used, the liquid medium were aqueous solutions of methylene blue and more complex organic compound in the form of humic substances. As a result of the destruction of hydrocarbon gas molecules in microwave discharge plasma new products such as hydrogen, ethylene, acetylene and carbon nanostructured material have been formed. In experiments on destruction of molecular compounds in aqueous organic solutions we used air, nitrogen and argon for plasma gases. It is shown that the process of molecular destruction in aqueous organic solutions in the microwave discharge plasma is based on oxidation-reduction reactions. It is found that the maximum efficiency of removal of organic compounds from the solution occurs when using air as the plasma gas.