Plant roots have evolved with the presence of rhizobacteria that can colonise the surface or interior of the plant. Some of these rhizobacteria are actively recruited by the plant and carry out particular functions, in particular in nutrient acquisition. Nitrogen-fixing bacteria form associations with many plant species, either as external associations or as symbiotic endophytes. The symbiosis between legumes and nitrogen-fixing rhizobia has been studied in most detail and is the most important contributor to nitrogen fixation in agriculture. This chapter highlights our current understanding of the molecular determinants of legume nodulation as well as challenges for improvements of biological nitrogen fixation in legumes and non-legumes. There is a need for connecting out knowledge of the molecular regulation of nodulation with field-based studies that take into account the interaction of nodulation with biotic and abiotic constraints. In addition, current approaches for engineering new symbioses are discussed.