Microbial mats are considered to be extremely thick biofilms. Chemolithotrophic and phototrophic bacteria build them. Microbial mats form layers that are composed of different microbial guilds whose activity is dependent upon the amount of light available and other resources like nutrients. Different organisms are living in the mat, and the order in which they are layered depends on nutrient transport controlled by diffusion. These various microorganisms form the layers that make up the microbial mat.

Microbial mats are declining in abundance due to competition of aquatic plants and metazoan grazers. Today, microbial mats develop only in marine environments, where competition is restricted. These environments are hypersaline or geothermal habitats. Because microbial mats grow only in extreme conditions and remote locations, it is difficult to study them today. Microbial mats are sensitive to changing light intensity. Light intensity significantly influences the chemical and biological structure of a microbial mat.

Cyanobacteria is the most abundant and versatile mat builders. They can grow in hot temperatures or cold temperatures. The cyanobacterial mats contain large numbers of primary producers. Primary producers use light to synthesize new organic material from CO2. Cyanobacteria, unlike microbial mats, grow in places that are easily assessable to scientists like Yellowstone or other thermal regions of the world.

Chemolithotrophic microorganisms also build mats. These mats are composed of filamentous sulfur-oxidizing bacteria, which grow on marine sediment. The chemolithotrophic mats oxidize H2S to support energy conservation and autotrophic reactions. The microbial mats on earth composed of Thioploca species on sediments of Chilean and Peruvian continental shelf are thought to be the most extensive microbial mats on Earth.

Microbial mats start as biofilms but as biofilms form on a surface they become more complex and diverse. The diversity reaches its maximum in a microbial mat.