Bacteria cause few infections in the oral cavities, other than pharyngitis given the impossibility of collecting a surface culture of these spaces without including the abundant indigenous flora, culture from lesions of these bacteria is of great importance for proper diagnosis. The indigenous microbiota plays an important role in health and diseases of humans and animals. Indigenous bacteria can survive in the oral cavity because they are less susceptible to or can avoid immune mechanisms. Oral diseases seem to appear after an imbalance among the indigenous microbiota, leading to the emergence of potentially pathogenic bacteria. The main disease caused by the oral flora are dental plaque, dental caries, gingivitis and periodontal disease yet they may also cause systemic disease also.