Legumes establish symbioses with wide range of beneficial soil microorganisms (BSM), which represents examples of various plant microbe mutualistic systems. This divergent category of beneficial microbes promotes plant development and offer shield from pathogens and pests. Arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis are the two most influential legume symbioses for agriculture. These two associations demonstrate high level of genetic and metabolic integrity, in comparison with other interactions with plant growth-promoting rhizosphere bacteria (PGPR) and beneficial endophytic bacteria. In last decade, a significant progress has been achieved in revealing the genetic bases of symbioses formation and functioning, so the knowledge of the plant genetic control over symbioses can effectively facilitate used for developing tools for genetic manipulation of the host or bacteria in order to enhance nitrogen fixation efficiency and breeding new varieties of legumes that are needed for sustainable agriculture. In this article, the present state of the developmental genetics of legume symbioses to be used for optimizing the broad spectrum of plant adaptive functions to improve sustainability of legume crop production is discussed.