A novel type of defense system was recently identified in bacteria: the CRISPR array and its associated gene products (Cas). The system inserts short DNA sequences, called spacers, derived from foreign nucleic acid molecules in between direct repeats, thus forming the CRISPR array. The transcribed spacers eventually serve as molecular guides for Cas proteins that monitor and destroy nucleic acids having sequences similar to those spacers. Thorough mapping of the functional components and regulators of the system in a single model organism will be extremely valuable for understanding its mechanism of action. Studying the interactions between bacteria and phages should highlight the evolutionary role of the system and its consequences for shaping ecological systems. These insights will lead to novel ways of exploiting the system to improve molecular biology tools, to protect fermenting bacteria from phage spoilage, to equip phages with anti-CRISPR warfare to fight bacteria, and to prevent horizontal gene transfer between pathogens. Here, I intend to systematically seek out new roles of the system and to identify fundamental mechanisms and components that allow the system to function efficiently. I will address fundamental questions such as how the system avoids sampling self DNA into the CRISPR array. In addition, I will pursue two revolutionary possibilities. One, that the CRISPR/Cas system is not merely an adaptive defense system against phages, but that one of its roles is to serve as molecular machinery for silencing specific harmful genes by generating small silencing RNAs without the need for Cas proteins. The other is to test the system’s ability to prevent horizontal gene transfer of antibiotic resistance genes in an effort to study the system’s ecological value, potentially for applicative uses. My proposed studies will allow deeper understanding of the system, and enable breakthroughs from both basic and applicative aspects of the CRISPR field studies.