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Endophytes are microorganisms that colonise the internal compartments of host plants without harming the host. In many cases, endophytic bacteria have been shown to provide several beneficial effects to their host plant, including growth-promoting activity, modulation of plant metabolism and phytohormone signalling that leads to adaptation to environmental abiotic or biotic stresses. Endophytic bacterial community structure is influenced by plant genotype, soil type, abiotic and biotic factors, such as environmental conditions and microbe–microbe/plant–microbe interactions. In addition, agricultural management practices, such as soil tillage, crop rotation, and fertiliser and pesticide applications have a major effect on the function and structure of the soil, rhizosphere and endophytic bacterial communities. Oilseed rape (Brassica napus L.) is an important break crop in cereal crop rotation and can significantly reduce the rate of ‘take-all’ fungal disease (Gaeumannomyces graminis var. tritici) and, as a result, improves the yield of subsequent cereal crops. Additionally, oilseed rape is the world’s third largest source of vegetable oil used for human nutrition and as a source of oil for biodiesel production. Therefore, the promotion of agricultural practices that maintain the natural diversity of B. napus endophytic bacteria is receiving attention as an important element for a sustainable agricultural system that ensures crop productivity and quality while reducing inputs. This chapter reviews the existing literature on the role of endophytic bacteria in oilseed rape crop production, agricultural factors influencing oilseed rape bacterial diversity and discusses how meta-omics is enhancing our understanding of the endophytic bacteria and their function.