Knowledge on the evolution of symbiotic bacteria elicited by their co-migration with host plants into the novel soil/climatic environments should be used as a conduit for constructing the beneficial plant-microbial systems applied in sustainable agriculture. Co-migration of leguminous plants and nodule bacteria (rhizobia) from the centers of origins into cropping areas often results in generating the Novel Symbionts (NS) via the “symbiotic” gene transfer from initial symbionts to the local soil or plant-associated bacteria. NS usually combine the low/zero activity of N₂ fixation with the high competitiveness for soil and nodular niches blocking the inoculation of leguminous crops by commercial strains. Mathematical simulation of legume-rhizobia interactions suggests that this effect may be due to retarding the evolution of NS towards the elevated N₂-fixing activity. Construction of coadapted “gene-for-gene” systems is a promising approach to ensure the competitive advantage of effective (commercial) rhizobia strains over the ineffective (NS, local) strains. This advantage may be ensured also by engineering the genes responsible for soil adaptations and nodulation competitiveness into the rhizobia genotypes capable of active N₂ fixation.