Major types of bacteria were traditionally classified by physical features or reactions to different types of staining. The advent of molecular genetics has allowed a more-careful division of the different groups of bacteria. Many scientists believe that the old classification of bacteria should be split into two or more kingdoms.

The highest classification of living things is kingdoms. Bacteria were once classified in one kingdom known as Protista, but many scientists argue that the old kingdom should be split into two kingdoms based on molecular genetic evidence. The new kingdoms would be true bacteria, Eubacteria, and ancient bacteria, Archaebacteria, that today survive in extreme environments. Some suggest a new phylogenetic division known as domains or superkingdoms, because the Archaebacteria are so distinct, they could be split into three kingdoms of their own: Crenarchaeota, the thermophilic bacteria; Euryarchaeota, halophilic and methanogenic bacteria; and Korarchaeota, found in hot springs.

For bacteria other than Archaebacteria, there are five distinct phylums, the next branch up the phylogenetic tree. The Proteobacteria are symbiotic with plants and help them fix nitrogen from the atmosphere. The Cyanobacteria are known as blue-green bacteria. Eubacteria are traditionally-classified Gram-positive bacteria and have cell walls that have different layers than other bacteria. The Spirochetes grow in spiraled colonies. The Chlamydiae are intracellular parasites.

Bacteria can be described as pathogenic (disease-causing) or non-pathogenic. They can also be described as Gram-positive or Gram-negative. This refers to whether or not they absorb a dye by Gram staining. Gram-positive bacteria lack an outer cell membrane, and peptidoglycans allow them to be stained with crystal violet. Gram-negative bacteria have an outer cell membrane but lack peptidoglycans, preventing them from being stained.