A current trend in the understanding of the pathogenesis of several human endogenous infections is to shift away from a reductionist paradigm to a holistic view of the microbial community as the unit of pathogenicity. Data brought about by studies on the pathogenicity of mixed infections, amalgamated with emerging information on physiological cooperative behavior of multispecies biofilms, bacterial interactions and food webs, and quorum-sensing systems reveal that the community outcome can be much more than the mere sum of its individual components. The concept of the community as pathogen is based on the widespread principle that teamwork is what eventually counts. Mounting evidence based on morphological and bacterial community profiling studies has demonstrated that apical periodontitis is a disease primarily caused by bacteria organized in biofilm communities adhered to the root canal walls. From the perspective of the single-pathogen concept, apical periodontitis can be considered as of no specific microbial etiology. However, based on the community-as-pathogen concept, it is possible to infer that, despite the high interindividual variability in endodontic microbial community composition, there are apparently some disease-related patterns. This article focuses on diverse ecological and pathogenic aspects of microbial communities, especially in relation to the pathogenesis of apical periodontitis. Therapeutic strategies based on ecological interference and other factors are also discussed. Future research should focus not only on the structure (species richness and abundance) of endodontic bacterial communities, but also on the application of methodological approaches that allow interpretation of the community behavior and function.