Periodontal diseases (gingivitis and periodontitis) are chronic bacterial infections with a remarkably high prevalence and morbidity. Periodontitis, in contrast to gingivitis, is not reversible, is associated with certain bacterial species and affects all of the soft tissue and bone that support teeth. Among the periodontal pathogens, species, such as Aggregatibacter (Actinobacillus) actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythensis, and several forms of uncultivable spirochetes play the major role in the pathogenesis. In severe chronic, recurrent and especially aggressive forms of periodontitis, diagnosis of the species involved and, whenever possible, an optimized evidence-based antimicrobial treatment is indicated. In order to monitor alarming bacterial changes in the periodontal pocket, several techniques, namely microscopy, culture, immunoassays, enzyme tests and DNA-based techniques, have been established and the methods are described in the first part of this review. In the second part, the selection and use of locally delivered (topical) and systemic antibiotics used adjunctively in periodontal therapy are discussed.