New insights in the microbial genetics of pathogenic oral micro-organisms and the development of a new array of molecular genetic techniques together have led to alternative strategies in the development of antimicrobial agents. In this article the importance of insights in microbial molecular biology for the prevention and treatment of (oral) infectious diseases is illustrated. Following the introduction of relevant terminology, the role of microbial genetics in developing of target-based anti-microbial drugs for prevention and treatment of (oral) infections is discussed. Subsequently, the impact of microbial genetics on vaccine development and several, mainly still experimental, prevention strategies are discussed.