The three components of taxonomy are classification, nomenclature and identification. Traditionally, bacterial classification and identification were performed based on the morphology and the biochemical data of the bacteria. In newer theories, or so-called natural concepts, the relationships between bacteria are based on the overall similarities of both the phenotypic and genotypic characteristics. The polyphasic taxonomy, or current taxonomy, describes the integration of all of the available genotypic, phenotypic, and phylogenetic information into a consensus type of general-purpose classification. When routine identification methods that are based on the biochemical tests fail, alternative procedures such as complete 16s rRNA gene sequence analysis are required. Although the results of 16s rRNA gene sequence analysis have not been fully discriminatory to differentiate closely related species, they may guide the additional analyses that are required for species identification. (Korean J Clin Microbiol 2012;15:79-87)