Remediation of the subsurface contaminated with petroleum products is the ecological problem on a world scale and a foreground direction of geoecological research in Ukraine. Remediation of contaminated vadose zone can be provided with the activity of microorganisms, mainly micromycets, whose features of location and vital activity depend on a depth, the level of contamination, aerobic conditions, etc. Practically, it is complicated to use artificial microbiological methods and natural remediation of contaminated subsurface due to microorganisms should be taken into consideration. Microorganisms oxidizing hydrocarbons are of particular interest. Field investigations were carried out within the fuel storage of the Boryspil airport where subsurface contamination with petroleum products was revealed in 1998. The research included sampling at contaminated and uncontaminated sites, quality analysis of petroleum product contains in soils and determination of the species composition of micromycets. Soil samples were taken in three wells at different depths – in the center of the contamination source at the depths of 0,1 m and 2,0 m (unsaturated zone) and 4,0 m (saturated zone), in the northern part of the fuel storage in the unsaturated zone at the depths of 0,1 m and 1,0 m, and out of the contamination source in the unsaturated zone at the depth of 3,7 m. Fungus culture determination data in soil samples indicate that variety of their forms depends on a contamination degree, a depth of sampling, lithology and water saturation. Regular monitoring should be carried out including soil sampling and determination of petroleum product contains to specify conclusions about natural remediation of contaminated soils due to life activity of microorganisms oxidizing hydrocarbons.