Recent studies show the major impact of airborne pathogenic microorganisms, particularly fungi. These pathogens contaminate the environment in both rural and urban areas as well as agricultural fields, which leads to the occurrence of various plant diseases. Fungi that travel faraway on a breeze can cause disastrous losses because of their ability to proliferate, especially to crops that are planted across wide areas. These diseases can spread substantially on several crops in the past decade. The progression of airborne plant diseases was influenced by major factors, i.e., cultivar susceptibility, pathogen genotype, climate including temperature, humidity, and moisture, planting patterns, plant structure, and development stage. Some fungal endophytes that reside inside plant tissues are recognized and applied in vivo on targeted plant surfaces to suppress the growth and development of fungal phytopathogens, thus increasing the disease control rate. Various studies have been conducted recently for controlling airborne pathogens through biological control methods due to the major losses caused by them worldwide. In this chapter, we will learn about the application of various endophytes as biocontrol agents as an alternative approach to fungicides as these cause detrimental effects on plants, soil and the environment due to chemical residues left by them and are costly to use. In comparison, endophytes are eco-friendly, effective against targeted phytopathogens and don’t cause any harm to plants. Hence they were tested in vitro and applied in vivo to control various airborne pathogens that cause several diseases in plants.