In addition to being widely distributed and dominant in the early stages development of many ecosystems, lichens are an important part of modern ecological systems, especially in rock, arid and coastal regions, the Antarctic and Arctic, and the tropics. In some areas, certain lichens are valuable economically as traditional foods and medicines. They serve as biological markers of air contamination. A lichen is a stable, ecologically required mutualism between an inhabitant population of extracellularly located unicellular or filamentous algal or cyanobacterial cells and an exhabitant fungal partner (the mycobiont). In many ways, the endolichenic fungi are similar to the endophytic fungi of vascular plants; they live inside the lichens, do not cause outward signs of disease. Saxicolous lichens exhibit antimicrobial, cytotoxic, and antioxidant activity. Lichens also play a role as bioindicators of nitrogen fixation. In this chapter, we will provide an overview of the saxicolous lichen and their relationship with endophytic fungi and the study of the diversity of endophytic fungi and the effect of different environmental conditions.