This chapter starts with a brief history of the growing public interest in the ecology of resistance genes and then moves on to a survey of some of the conceptual problems that have emerged. It focuses on a few groups of bacteria that are major players in the oral and intestinal ecosystems of humans and animals, the obligate anaerobes. Perhaps the first modern example of the sudden importance of understanding the ecology of antibiotic resistance genes arose in connection with the debate over the safety of GM plants. Studies have shown that many soil bacteria are naturally transformable, although it is still unclear what significance this fact has in the overall ecology of antibiotic resistance genes. Bacteria in and on the human body have participated in the distribution of resistance genes. An interesting case in point is the population of bacteria that makes its home in the periodontal pocket, the region between the gums and the roots of the teeth. Prominent among these are the Porphyromonas and Prevotella species. These bacteria have been of particular interest in dentistry because they are thought to be instrumental in the development of periodontal disease, the main cause of tooth loss in adults. Currently, the treatment for periodontal disease is surgery that cuts into the gums, exposing the buried surface of the teeth to allow scraping of the plaque that has accumulated there and is causing inflammation.