The oral microbiome plays a crucial role in the establishment and maintenance of oral health. Major disturbances in the interactions between this microbiome, the microenvironment, and the host may lead to the development of oral diseases. A large proportion of infectious diseases that affect humans are caused by organisms living in biofilms. This is also the case for oral infections such as dental caries, periodontal diseases, and endodontic and fungal infections. In this review, new concepts regarding the role of the oral biofilm in the etiopathogenesis of these diseases are presented, and a more ecological view of pathogenic communities as causative agents of oral diseases is discussed. We believe that a better understanding of oral biofilm physiology and ecology will provide insight for the development of new cost-effective diagnostic tools, as well as preventive and therapeutic strategies for the management of these infections.