Since the late 1990’s, advances in molecular technologies allowed the DNA sequencing of microbial communities. This enabled the identification of the genetic background of all the microbes – bacteria, fungi, protozoa and viruses – that live associated within a plant (endophyte) or attached to seed, leaf or roots of a plant in a particular environment and make up its microbiome, e.g., the diverse community of microorganisms living in and on it. Then, for plants, the “holobiont” concept emerged and was described as “a unit of biological organization composed of a host and its microbiota” (Margulis, 1993; Bordensteim et al., 2016). It is associated with its hologenome which is the complete genetic content of the plant host genome, its organelles’ genomes, and its microbiome which together constitute the genetic conception of the living beings. In the same way as all agronomical developments which support the industrial agriculture since the 19th century have been inspired by the chemical vision of life, plant breeding for this type of agriculture has been strongly based on the science of genetics and has progressed thanks to developments in molecular biology. Nowadays, the scientific community aims to promote an adapted vision of plant breeding for organic agriculture that has been called “organic plant breeding”. This vision advocates a holistic approach and comes back to the foundation and the principles of organic agriculture thanks to the holobiont concept of living beings.