In this review, references to the use of microorganisms in the process of plant domestication, genetic improvement, and production of traditional and improved varieties have been identified. The domestication process may have had an adverse impact on the composition and functions of the associated microbiota and the microbiota associated with plants influences multiple regulatory processes of plants that together define their phenotype. According to scientific evidence, to increase agricultural production and the sustainability of production systems, future research should develop breeding methods that optimize the symbiosis between plants and microorganisms, to produce new plant phenotypes that result in the production of enough food to meet the needs of the human population.