The dental biofilm is a complex bacterial ecosystem that undergoes evolution, maturing and development, and thus leads to odontogenic infection. The infection is normally located in the tissues of the dental organ itself, and follows a chronic course of evolution. However, bacterial pathogens express virulence factors in the biofilm, and this together with changes in host immunity, may cause clinical exacerbations and spread of infection to other areas of the body. Odontogenic infection management should take into consideration the fact that therapeutic success lies in the control of the infectious aetiologic agent, using mechanical-surgical debridement and/or antimicrobial therapy. Debridement techniques have a fundamentally quantitative effect (by reducing the size of the inoculum) and therefore if these techniques are used alone to control infection, despite an initial clinical improvement that is sometimes prematurely considered as therapeutic success, odontopathogens may persist and the process may recur or become chronic. Microbiological examination may be helpful in defining therapeutic success in a more reliable way, it could define the prognosis of recurrence more precisely, and could enable the most appropriate antibiotic to be selected, thus increasing therapeutic efficacy. Antimicrobial therapy brings about a quantitative and qualitative change in the bacterial composition of the biofilm, in addition to being able to act on sites that are inaccessible through mechanical debridement. However, incorrect antimicrobial use can lead to a selection of resistant bacterial species in the biofilm, in addition to side effects and ecological alterations in the host. In order to minimise this risk, and obtain maximum antimicrobial effect, we need to know in which clinical situations their use is indicated, and the efficacy of different antibiotics with regard to bacteria isolated in odontogenic infection.