This study investigated the endophytic fungal diversity associated with Salvia persepolitana, a medicinal plant endemic to Iran. Plant specimens were collected from Khuzestan province of Iran. Taxonomically verified using morphological keys and herbarium comparisons. Endophytic fungi were isolated from root and lower stem tissues. A total of 35 fungal isolates were obtained, with a majority (74%) derived from root tissues. Fungal genomic DNA was extracted, and internal tran scribed spacer and large subunit rRNA regions were amplified and sequenced for molecular identification. Sequence analy sis revealed dominance of Ascomycota (97.14%), particularly within the Dothideomycetes and Sordariomycetes classes; Pleosporales and Hypocreales orders; Pleosporaceae and Nectriaceae families. The most common genera were Fusarium (40%) and Alternaria (37.14%). Phylogenetic analysis based on the Maximum Likelihood approach identified a total of 21 distinct fungal species. Among these, Alternaria alstroemeriae and Alternaria angustiovoidea were the only taxa recovered from both root and aerial tissues, suggesting a degree of tissue specificity among the endophytic community. Root tissues harbored greater fungal diversity relative to aerial parts, highlighting differential colonization patterns. The dataset encompasses both previously recognized and novel fungal associations, thereby substantially advancing current knowl edge of endophytic interactions within the genus Salvia. Except for Fusarium avenaceum, Fusarium redolens, and Phoma herbarum, the remaining 18 taxa represent new records for the genus. Moreover, several species including Fusarium hostae, Alternaria conjuncta, Alternaria malorum, Cladosporium cucumerinum, Diaporthe ambiguea, and Xenodidymella camporesii are reported here, to the best of our knowledge, for the first time as endophytes in any plant host.

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