Microbiological indication of soil over Stepnovskoye underground storage of natural gas was carried out on the basis of estimating the number of heterotrophic, hydrocarbon-oxidizing and methylotrophic bacteria. Increased number of microorganisms of test physiological groups were found, indicating the admission of methane in the upper layers of the soil. The possibility of using hydrocarbon-oxidizing and methylotrophic bacteria for environmental monitoring of soil in the areas of natural gas storage facilities was shown.