Caper is one of the plants that has long been used in Iranian traditional medicine as a pain reliever, as well as in the treatment of rheumatism and gout, and has been shown to have an analgesic effect. Alternaria fungus is an international fungus widely spread in soil and organic matter. This fungus includes saprophytic, endophytic and pathogenic species. At least 268 metabolites have been reported from Alternaria fungi in the past few decades. In this research, the isolation of root endophytes of Caper from Abbar-Gilvan region (Zanjan province) was investigated. After transferring the plant to the laboratory and surface sterilization of the roots, the endophytes isolation was carried out and its molecular detection was investigated. The results showed that Alternaria alternata was identified as endophytic, and the conidiophores were relatively short, and the conidiums which often lacked the tip, were characterized by a secondary conidia with one to two cells. The conidia chain was often diagnosed on conidiophores with an average length (up to 20 conidiums). The molecular detection of this fungus further confirmed its morphological diagnosis. Due to its ability to produce biologically active metabolites, this fungus can be useful for future studies and can be used by pharmaceutical and healthcare industries.
