All macro-organisms (e.g., forest trees, plants, and animals) live in close association with a diverse range of microbial symbionts. The term microbiota has been used to describe this ecological community of archaea, bacteria, fungi, and protists associated with a given organisms, its organs and tissues. Microbiome refers to the entire assemblage of all microbial genomes of the microbial community (microbiota) associated with certain environment or organism. The inherent features of this close association between microbes and their hosts can be commensalism, parasitism, mutualism or endophytic. Research on microbiome of forest biomes has attracted much attention in recent years but still lags far behind comparable knowledge on human and agricultural crop microbiomes. Many of the microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Despite a significant progress achieved in our understanding of microbiome, very little is known about the beneficial effects of endophytes particularly for the least studied forest trees. There are several ways by which endophytic microorganisms can have beneficial roles in promoting forest tree health including protecting their tree hosts against pathogens. Endophytes can enhance plant resistance by triggering and priming host defensive reactions. Endophytes can promote plant growth by producing beneficial secondary metabolites (e.g. phytohormones) or providing nutrients (e.g. phosphorus). Endophytes can compete with pathogens by colonization of shared niche to restrict pathogen invasion or can produce antagonistic metabolites. Endophytes could provide several opportunities for application in integrated pest management (IPM) to gain sustainable forestry practices. However, at the other extreme are microbial phytopathogens of forest trees that use effectors to modulate host defenses and cause disease. Using the root and stem rot pathogen (Heterobasidion annosum) as a model, I would highlight our concerted efforts to identify and functionally characterize the pathogenicity factors of this conifer pathogen.