The ubiquity of endophytic microorganisms is an accepted fact nowadays and the possibility of using it in agriculture keeps attracting attention of scientific community. In contrast to rhizospheric (living on root surface) and phyllospheric (colonizing aerial parts of plants) members of plant-microbial interactions endophytes are able to establish closer relationships with host-plant, in some cases strongly influencing its phenotype, bringing benefits. However, these microorganisms do not form any specific structures like nodules in case of symbiosis between legumes and rhizobium bacteria. Having a great amount of functions including phytohormone level modulation, vitamins production and nutrient supply improving, endophytes could serve as a basis for biofertilizer, which could potentially minimize the necessity of mineral fertilizers, thus reducing the negative impact of the latter on soil fertility, biodiversity and human health. Our main aim here is to highlight the question of functional significance of endophytes and endophytic bacteria in particular, as well as the way of its application in agriculture and to identify key points in understanding biology of these organisms. In this review we will consider such aspects of plant-endophytic symbiosis as biodiversity of legume and non-legume endophytes, ecology of endophytes and some ways which are commonly in use by studying these microorganisms.