Aconitum heterophyllum is a rare perennial herb from Kashmir Himalayas. Due to its threatened status and dependence on its environment, the plant was examined for any potential endophytes, which is of utmost importance for bioprospection. In the current study, endophytic fungal diversity associated with A. heterophyllum was examined, and 328 fungal isolates were found in the plant's leaf, stem, and root tissues. Twelve (12) endophytic fungal species were identified utilizing, molecular analysis of the nuclear ribosomal DNA Internal Transcribes Spacer (ITS), rLSU, and rSSU sequences. Maximum likelihood analysis was used to determine the phylogenetic connection between each isolate. The genera Arthrinium, Chaetomium, Purpureocillium, Alternaria, Penicillium, Aspergillus, Cladosporium, and Bjerkandera species dominated the ascomycete and basidiomycete fungal endophytes., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)