For the arrangement of micro-organisms in groups according to their similarity, 3 notions are distinguished:

1. Taxonomy – The science of classifying bodies; operates with taxons (levels in the hierarchy of a classification).

In order of their ranks, the main taxonomic groups (taxons) are:

• Regn – The most comprehensive systematic category used in the classification of the living world; the five Regn system developed by Robert H. Whittaker (1969) is accepted by a large number of specialists.
• Phylum/Filum – subdivision of animal, consisting of a group of classes having a general plan of common organization;
• Class – Subdivision of Phylum, consisting of a group of orders;
• Order – Subdivision of the class, consisting of several related families;
• Family – Subdivision of the order, comprises several related genera;
• Genus – consisting of several species with common origin, which differs from another taxon of the same rank;
• Species — The fundamental taxonomical unit of classification and evolution, which groups individuals who come from a common ancestor and have distinct characteristics, and which can cross among  themselves by giving descendants.

2. Classification – Arranging bodies according to similarities or related, in groups or taxa representing ranks or levels in the hierarchy of a classification;

• Phenotypic – Reunion of micro-organisms based on common phenotypic characters (morphological, culture, physiological, biochemical, antigenic).
• Genotypic – Depending on the degree of approval of the nucleotide sequences of microbial DNA, ribosomal RNA and the relative guanine + cytosine (GC%) content of purified DNA.
• Philogenetic – Determines the location of microorganisms in a phylogenetic tree and is based on the study of fossils or HLA.

According to the latest International Classification of Microorganisms (Bergey’s Manual of Systematic Bacteriology, 2001) are distinguished:

• Acellular forms (viruses, viroids, prions)
• Cellular forms, divided into 3 areas with a reference to mobile organization:

-Bacterial field – with Prokaryote-type cellular organization, with all types of bacteria (gram positive, Gram negative and mycoplasma).

-The field of Archaea – prokaryotes, with habitat in extreme conditions, which at the molecular level are more similar to eukaryotes than with bacteria;

-Eukarya Field – with cellular organisation of eukaryotic type, includes microfungi, protozoa and microalgae.

3. Nomenclature – The scientific system of naming taxonomic groups according to international rules.

For the designation of the scientific or specific name of the species is used the binominal system (introduced by Swedish naturalist Carl Linné-the parent of the taxonomy) which consists in the name of a body using two words written in Latin or transliterated in Latin from other languages – the first is the type, and is always written in capital letters, and the second is the species.

The taxons nomenclature is originally a Greek or Latin noun, which defines the most obvious character of the studied microorganisms, plus a certain Latin suffix.