The systematics of bacteria is a fundamentally important discipline of microbiology. The huge metabolic diversity and horizontal gene transfer tendencies of bacteria make it difficult to line them in a systematic manner. The current bacterial species classification is based on a combination of genotypic and phenotypic properties. More than 6200 species of prokaryotes have valid names according to the International Committee on Systematic Bacteriology (ICSB). In this review, approaches and techniques applied for identification based on biochemical and physiological investigations of bacteria, chemotaxonomic, mass spectroscopic techniques and the genotypic methods are evaluated. The combined approaches, classic culturing methods and innovative molecular approaches provide more reliable results for the identification of prokaryotes.