Endolithic micro-environments of rock are unique, ranging from high mountains and deep-sea floors to deserts and the Arctic and Antarctic regions colonized by high diversity of microbes. Endolithic microorganisms survive the extreme environmental conditions of rock pores and fissures with their survival strategies. In addition, the bulk rock provides mineral nutrients and protects the inhabitants from drastic ecological stresses from changes in the local conditions. Thus, endolithic microbes are at pivotal interface between geology and biology that offers a model system for unique microbial ecology, astrobiology, and geomicrobiology. This review provides comprehensive information on the diversity of endolithic microbial communities in cold, arid, aquatic, and terrestrial ecosystems and their survival strategies under ecological stresses. Furthermore, rock architecture for the colonization of endoliths, their biochemical functions and potential applications are discussed. It is clear that integrating modern molecular methods with physical and chemical analytical instrumentation will further advance our knowledge about endolithic microbial ecology, diversity, unique adaptive mechanisms, ecological functioning, and biochemical processes that shape the past, current, and future biosphere.