To feed the increasing population of the world farmers and the crop growers rely on the use of synthetic chemicals as pesticide and fertilizer for the enhancement of soil nutrition, pest and disease management of the crops to increase the yield. However, these synthetic chemicals further aggregate the existing problem of environmental contamination, food safety, and are more harmful to the entire ecosystem. Owing to the ability to promote the growth and development of the plant and protection against various stresses and diseases the only technology to meet all the challenges is the use of beneficial microorganisms. Recently the development of fungi as the biocontrol agents and biofertilizers is increasing rapidly among the scientific community. Fungi such as Arbuscular mycorrhiza, Piriformospora indica, Penicillium, and various others have proved to play a beneficial role in nutrition enhancement, phosphate solubilization, and protection against various stresses by establishing a symbiotic relationship with the host plants. Several fungi are mass produced and commercially available in the market to promote the growth and development of plant as well as to increase the plant defense mechanism. This chapter focuses on various fungal communities that play a significant role in the overall growth and yield of the crop.