Leguminous plants have a genetic system that provides interaction with different beneficial soil microorganisms (BSM). The system has been formed on the basis of the genetic mechanisms that had arisen during the co-evolution of plants with arbuscular-mycorrhizal (AM) fungi and appeared to provide pre-adaptations for further evolution of interaction with various BSM. A concept of the use of BSM in sustainable agriculture is proposed, which postulates an establishment of the multi-component beneficial plant-microbe communities based on varieties of legumes with high potential for interaction with the BSM.