Agricultural microbiology is presented as a synthetic research field responsible for knowledge transfer from general microbiology and microbial ecology to the agricultural biotechnologies. The major goal of agricultural microbiology is a comprehensive analysis of symbiotic micro-organisms (bacteria, fungi) interacting with agriculturally important plants and animals: here we have focussed on plants. In plants, interactions with micro-organisms are diverse, ranging from two-partite symbioses (e.g. legume–rhizobia N2-fixing nodular symbioses or arbuscular mycorrhiza) to multipartite endophytic and epiphytic (root-associated, phyllosphere) communities. Two-partite symbioses provide the clearest models for addressing genetic cooperation between partners, resulting in the formation of super-organism genetic systems, which are responsible for host productivity. Analysis of these systems has now been extended considerably by using the approaches of metagenomics, which allow the dissection of taxonomic/population structures and the metabolic/ecological functions of microbial communities, which have resulted from the adaptation of free-living, soil microflora in the endosymbiotic niches. Both beneficial (nutritional, defensive, regulatory) and antagonistic (biocontrol) functions expressed by symbiotic microbes towards their hosts are the potential subjects of effective agronomic use. A fundamental knowledge of the genetics, molecular biology, ecology and evolution of symbiotic interactions could enable the development of microbe-based sustainable agriculture. This could achieve: (a) an improvement of major adaptive functions and productivity in crop plants by manipulating their microbial cohabitants; (b) partial or even full substitution of ecologically hazardous agrochemicals (mineral fertilizers, pesticides) by microbial preparations; (c) a decrease in the cost and an improvement of the quality of agricultural products.