Molecular soil science is a separate section of soil science. The concept of molecular soil science is referred to those soil researches, which study molecular processes (mechanisms) and their development on meso- and macro level of soil properties (morphological and physical), and also in ecological functions. Objects of molecular soil science are molecular mechanisms, soil matrix and processes of compartmentation. Molecular mechanisms are the chemical reactions with particular parameters: composition of ions, molecules, factors of selectivity, solubility constants, reaction velocity, paramagnetic centers, catalytic reactions, isomorphous substitutions, exchange reactions, complexing of mineral and humus substances. To molecular processes it is possible to relate all particular reactions taking place in soils and also formation of electrical fields in soil, magnetic susceptibility in upper soil horizons, processes of diffusion and processes of the synthesis of minerals under the effect of organisms. All molecular reactions can be divided in two groups: Chemical reactions taking place in soil and changing some properties (usual chemical reactions) and reactions which result to forming the soil macro properties as morphological, physical, structural and aggregates. In practice soil scientists study result of soil processes. However connection between results and molecular processes is not cleared. For example, chlorite in soils is the result from reactions of synthesis or from rock weathering. Carbonates in soils are the finish product of humus mineralization or result of salinization. Fe-Mn concretions are the product of microbiological activity or physic-chemical processes. Genesis of metallic spherules with magnetite is also discussed. It is affected by microorganisms or chemical processes or pollution or space area. Most of these reactions and interactions are connected to the soil matrix. Soil matrix is characterized by active centers (acid and basic nature) with the differing forces (from strong to weak). The diversity of active centers and clasters on the soil surface forms the differences compartments in which molecules, ions and microorganisms concentrate, specific adsorption of substances take place. These processes result to the division of soil matter and to the formation of soil profile. Kompartmentation in soil are the processes of ordinary separation of matter, particles, atoms and molecules in soil space and time. It creates and increases the diversity of soil matter and is very important in plant and microorganisms nutrition. The main goal of molecular soil science is to revile the links between molecular processes (mechanisms) and the meso- and macro level of soil properties (aggregates, horizons and profile). Thus, the first problem of molecular soil science is to study molecular processes, soil matrix and kompartmentation in soil. The second problem is to study the transmission mechanisms of soil properties between structural levels. In biological systems and organisms the reflection of molecular properties in whole organism includes so processes as matrix synthesis, replication, and transcription. In abiotic environment (crystals) there are specific mechanisms of transmission the information from atom to whole crystal: symmetric, transmission, epitaction and etc. In soils the structural parameters (porosity, specific surface and number of contacts) are very important for transmission mechanisms the soil properties between structural levels. Microscopic units carrying the information on the soil matrix can be active elements at its surface – centers and clusters. It is proved that next processes and mechanisms exist in soil formations: 1) Soil formation is characterized by the unidirectional process of organomineral matrix formation on mineral substratum. 2) Specifically of soil science structure is in aggregate formation. 3) Matrix humus formation is a function of mineral matrix. The matrix structural effect is appeared in the ability of the mineral matrix to influence physical characteristics of organomineral matrix. 4). Complementarity appears in donor-acceptor or acid-base interactions and fragmentary change in humus molecules. 5) The mechanisms of stability are buffer capacity, strength, adsorptive and etc. 6) In soil, the alternative to enzymes are the abiotic catalysts (clay minerals, oxides, hydroxides, salts, organic compounds) and immobilized by soil particles ferments. Thus, molecular soil science study soil reactions and their development on meso- and macro level of soil properties (morphological and physical) and also in ecological functions. Soil formation is the formation of organomineral matrix which determined all level of soil structure organization. Active centers of soil matrix can be of different functionally groups. The localization of soil matter, differentiation and heterogeneities of soil profile are controlled by processes of compartmentation.