The legumes have a genetic system that provides interactions with beneficial (for crops) soil microorganisms (BSM). This system is formed on the basis of genetic mechanisms, which developed during co-evolution of plants with arbuscular mycorrhizal (AM) fungi and provided preadaptation to further evolution of interactions with BSM. A concept of BSM use in sustainable crop production is suggested. This concept implies the creation of multicomponent plant-microbe communities on the basis of legume cultivars with high potential of interaction with BSM.