The importance of horizontal gene transfer (HGT) in bacterial evolution is evident from the retrospective analyses of bacterial genomes, which suggest that a substantial part of bacterial genomes is of foreign origin. Another line of evidence that supports the possibility of rapid adaptation of bacteria through lateral gene exchange is the history of antibiotic use by humans. Within a very brief period of the 'antibiotic era' many bacterial pathogens were able to acquire the mechanisms allowing them to withstand the selective pressure of antibiotics. And, finally, field and microcosm studies allowed monitoring HGT events in situ. In this chapter, a brief overview of the milestones of mobile genetic elements (MGEs) research is given, followed by discussion of the conceptual framework development. Then the occurrence and diversity of MGEs as well as the frequencies of HGT in terrestrial, aquatic, intestinal and biofilm communities are described. The role of environmental factors that may affect MGE-mediated HGT in these ecosystems is also discussed.