Besides a diffuse research activity on drug discovery and biodiversity carried out in natural contexts, more recently investigations concerning endophytic fungi have started considering their occurrence in crops based on the major role that these microorganisms have been recognized to play in plant protection and growth promotion. Fruit growing is particularly involved in this new wave, by reason that the pluriannual crop cycle implies a likely higher impact of these symbiotic interactions. Aspects concerning occurrence and effects of endophytic fungi associated with citrus species are revised in the present paper.