These include algae, fungi, bacteria and microfauna and their population is the largest among living beings. (Biodiversity Guide to Pakistan 1991) However, some studies suggest that only 10% of the population have been studied through available methods. Microbes are important for cycling of elements such as carbon and nitrogen, and as such contribute to soil fertility and nutrient mobility for crop production. In Pakistan the descriptions of microbes is limited.

Fungi exist in the country in the form of 4500 species and algae have a total of 775 species. Bacteria have also been isolated including some from extreme  environments. (Biodiversity Guide to Pakistan 1991)