The global occurrence of plant root-associated fungal endophytes and their great abundance in many habitats necessitate studies to decipher their potential functions. Improved understanding of the basic endophyte ecology including host range, host preference, and host responses to endophyte colonization has been made possible through populations of endophytes (e.g., Periconia macrospinosa and Microdochium sp.) isolated from North American native tallgrass prairie. The recent demonstration of the endophyte symbiosis of the model plant Arabidopsis thaliana has provided additional tools to further elucidate the ecology of these endophytes. The availability of a large number of Arabidopsis ecotypes and mutants, microarrays, and databases allows the molecular dissection of endophyte symbiosis to better understand the importance of fungal endophytes in host nutrient uptake, defenses, and/or responses to pathogens and stress. In this chapter, we discuss the ecology and functions of endophytic fungi through experiments utilizing the Arabidopsis model system. We draw parallels with another deeply dissected Piriformospora indica root endophyte symbiosis, which has been demonstrated to promote growth of model and non-model plants.