The aim of this paper was to evaluate strategies for periodontal therapy from the perspective of periodontal disease being a consequence of microbial colonization of the periodontal pocket environment. In classic bacterial infections the diversity of the microbiota decreases as the disease develops. In most cases of periodontitis, however, the diversity of the flora increases. Most incriminating bacteria are thought to harm tissues significantly only if present in high numbers over prolonged periods of time. Clinical trials have repeatedly demonstrated that scaling and root planing, a procedure that aims to remove subgingival bacterial deposits by scraping on the tooth surface within the periodontal pocket, is effective. At present, for the therapy of any form of periodontal disease, there exists no protocol with proven superiority, in terms of efficiency or effectiveness, over scaling and root planing plus systemic amoxicillin and metronidazole. Some exponents advocate rationing these drugs for patients with a specific microbial profile. However, the evidence for any benefit of bacteriology-assisted clinical protocols is unsatisfactory. Treated sites are subject to recolonization with a microbiota similar to that present before therapy. The degree and speed of recolonization depends on the treatment protocol, the distribution patterns of periodontal microorganisms elsewhere in the oral cavity and the quality of the patient's oral hygiene. To limit the use of antibiotics and to avoid accumulation of harmful effects by repeated therapy, further efforts must be made to optimize procedures addressing the microbial colonization and recolonization of the periodontal pocket.