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Fungal endophytes are a rich source of functional metabolites. In particular, the different species of the genus Alternaria stand out for their arsenal of metabolites, which have roles as antimicrobial molecules, antioxidants; as well as activities against HIV or cancer or diabetes. This review will highlight on selected aspects of the fungal endophytes of Alternaria species: their widespread distribution, and the role of their metabolites with pharmaceutical or agronomical importance. The family plants associated with Alternaria species, their bioactive compounds and biological activity to date are examined.