The recent explosion of oral microbiome sequencing studies has revealed unprecedented insights into the genetic content contained in the oral cavity. Such studies have identified countless uncharacterized organisms as strongly associated with various states of oral health and disease. Furthermore, transcriptomic, proteomic, and metabolomic studies have all revealed complementary functional phenotypes produced by these same communities. The looming challenge in the field is to translate these phenomenological descriptive analyses into molecular mechanistic descriptions. For this to occur, it will first be necessary to adapt a broad diversity of understudied oral microbes for detailed molecular microbiology and ecology research. Thus, in the current chapter, we provide a comprehensive overview of the molecular microbiology and ecology techniques that have played critical roles in the current molecular understanding of the oral microbiome and its host interactions. The described assay systems and technologies should serve as useful templates to help catalyze new research targeting the plethora of uncharacterized and understudied members of the oral microbiota.