Many characteristic features are used in classifying and identifying microorganisms. In general, these characteristic features have been divided into two major categories such as classical and molecular characteristics.

Classical characteristics

The classical type such as morphological, physiological, biochemical, ecological and genetic characteristics have been widely employed to study microbial taxonomy and it also provide phylogenetic information of microorganisms.

Morphological features are important in microbial taxonomy for many reasons. Morphology is easy to study and analyze both eucaryotic and procaryotic microorganisms. Many different morphological features are used in the classification and identification of microorganisms. Some of these features are cell size, cell shape, colonial morphology, ultrastructural characteristics, staining behavior, cilia and flagella, mechanism of motility, color etc.

Physiological and metabolic characteristics are very useful because they are directly related to the nature and activity of microbial enzymes and transport proteins. Because proteins are gene products, analysis of these characteristics provides an indirect comparison of microbial genomes. Some of the physiological and metabolic characteristic features are carbon and nitrogen sources, cell structure, energy sources, fermentation product, nutritional type, growth temperature optimum and range, luminescence, motility, osmotic tolerance, oxygen requirements, pH optimum and growth range, photosynthetic pigments, salt tolerance, sensitivity to metabolic and antibiotics etc.

Microorganisms are well associated and growing in terrestrial fresh water and marine environments. The taxonomically important ecological properties are life cycle patterns, the nature of symbiotic relationship, the ability to cause decease in particular host and habitat preference such as the temperature, pH, oxygen and osmotic concentration.

Most eucaryotes are able to reproduce sexually, hence genetic analysis has been of considerable usefulness in the classification of these type of microorganisms. However, procaryotic do not produce sexually and chromosomal gene exchange (through transformation and conjugation) is sometimes useful in the classification of procaryotes.

Molecular characteristics

The recent molecular approaches such as comparison of protein, nucleic acid base composition, and nucleic acid hybridization and sequencing are the most powerful molecular tools have been employed to study the taxonomy of some microbial groups, especially important for the procaryotic taxonomy.

Classification on their risk categories 

Harmless microorganisms
Micro-organisms that have never been identified as causative agents of disease in man and that offer no threat to the environment.

Low-risk microorganisms
Micro-organisms that may cause disease in man and might, therefore, offer a hazard to laboratory workers. They are unlikely to spread in the environment. Prophylactics are available and treatment is effective.

Medium-risk microorganisms
Micro-organisms that offer a severe threat to the health of laboratory workers but a comparatively small risk to the population at large. Prophylactics are available and treatment is effective.

High-risk microorganisms
Micro-organisms that cause severe illness in man and offer a serious hazard to laboratory workers and people at large. In general effective prophylactics are not available and no effective treatment is known.

Environmental-risk microorganisms
Micro-organisms that offer a more severe threat to the environment than to man. They may be responsible for heavy economic losses. This group includes several classes, to accomodate plant pathogens.

Classification of Microorganisms in Corrosion Microorganisms can be categorized according to oxygen tolerance

• Strict (or obligate) anaerobes, which will not function in the presence of oxygen.
• Aerobes, which require oxygen in their metabolism.
• Facultative anaerobes, which can function either in the absence or presence of oxygen.
• Microaerophiles, which use oxygen but prefer low levels.
  

Strictly anaerobic environments are quite rare in nature, while strict anaerobes are commonly found flourishing within anaerobic microenvironments in highly aerated systems.

For example, corrosion (oxidation of metal) can only occur if some other chemical is present to be reduced. In most environments, the chemical that is reduced is either dissolved oxygen or hydrogen ions in acids. In anaerobic conditions (no oxygen or air present), some bacteria (anaerobic bacteria) can thrive. These bacteria can provide the reducible chemicals that allow corrosion to occur. That's how the limited corrosion that was found on the hull of the Titanic occurred. The right picture shows a "rusticle" removed from the hull of Titanic. 

According to their metabolism

• The compounds or nutrients from which they obtain their carbon for growth and reproduction.
• The chemistry by which they obtain energy or perform respiration.
• The elements they accumulate as a result of these processes.

Bacteria can be classified  is by shape. These shapes are predictable when organisms are grown under well defined laboratory conditions. In natural environments, however, shape is often determined by growth conditions rather than pedigree.

Examples of shapes are ( Right figure denotes Bacellus anthracis)

• "Vibrio," for comma shaped cells
• "Bacillus," for rod shaped cells
• "Coccus," for round cells
• "Myces," for fungi like cells