Apple replant disease (ARD) is a major problem in all the apple-growing areas of the world. It is a complex problem. The exact cause of the problem is unknown, but soil biotic factors play a major role. The repeated cultivation of same crop on same land and exhaustion of nutrients of soil, persistence of soil-borne pathogens and changes in the pH of soil. Symptoms include stunting of tree growth with short internodes, small and light green rosette leaves, development of few lateral or feeder roots, underdeveloped root systems, decayed and discolored roots, poor establishment and severe disease results in the death of young trees and, sometimes, whole orchards. The endophytes provide direct benefits to host plants as they live in close proximity. Once they enter inside the host tissue they get easily established as they feel no competition with other microorganisms. Endophytes have the capacity to produce different secondary metabolites, which saves the host plants from biotic and abiotic stresses the host plants become resistant to both biotic and abiotic stresses. An interesting facet of the interaction between endophytes and their hosts is the capacity of many microorganisms to improve the plant’s resistance by providing several bioactive metabolites. Therefore, the exploitation of soil microbial endophytes for the management of ARD is an important strategy.