Microbiological characteristics of the zonal soils of Moldova were found to be sensitive enough to reflect both the pedogenetic differences between the studied soil types and subtypes as well as the consequences of soil agricultural management in the Republic. The current agricultural practices were demonstrated as unable to maintain favourable microbiological conditions in soil and, as a result, to prevent degradation of soil organic matter. The urgent need to implement the principles of sustainable agriculture by taking into account the peculiarities of functioning of the soil ecosystem is discussed.