Development of mutualistic symbioses between ectomycorrhizal fungi and their host trees involves multiple gene networks that are involved in a complex series of interdependent, sequential developmental steps. Through secreted signals and nutrient interactions, rhizospheric bacteria play a major role in the development of mycorrhizal symbioses. Current research into symbiosis development and functioning is aimed at understanding these plant–microbe interactions in the framework of environmental, developmental and physiological processes that underlie colonization and morphogenesis. After a brief introduction to the ectomycorrhizal symbiosis, the present chapter aims (1) to highlight recent work on the early signal exchange taking place between symbionts and their associated bacteria, and (2) to sketch out the way that functional genomics is altering our thinking about how soil microbes alter host functioning during ectomycorrhizal root development.