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Background  Present study focuses on diversity and distribution analysis of endophytic fungi associated with different tissues of the  Monarda citriodora  Cerv. ex Lag. (Lamiaceae/Labiatae). Anticancer and antimicrobial potential of isolated endophytes have also been investigated.    Results  A total of twenty eight fungal endophytes belonging to 11 different genera were isolated from this plant. All the endophytic fungi belonged to the Ascomycota phylum. The leaves were immensely rich in fungal species, while roots showed the highest tissue specific fungal dominance. Out of 28 fungal species, 72% endophytic extracts were found cytotoxic against one or more human cancer cell lines. The most prominent anticancer activity (IC 50  value <10 μg/mL) was shown by MC-14 L ( Fusarium oxysporum ), MC-14 F ( F. oxysporum ), MC-18 L ( Aspergillus fumigatus ), MC-24 L ( Cladosporium tenuissimum ), MC-25 L ( Fusarium  sp.), MC-26 F ( F. oxysporum ) extracts. 75% of the extracts showed antimicrobial activities in agar disc-diffusion assay and 27% in the tube dilution method (MIC <100 μg/mL) respectively against the tested pathogens. Extracts of MC-14 L ( F. oxysporum ) and MC-18 L ( A. fumigatus ) displayed broad spectrum antimicrobial activity.    Conclusions  These results indicated that  M. citriodora  harbors a rich fungal endophytic community with anticancer and antimicrobial activities. The isolated endophyte MC-24 L ( C. tenuissimum ) has the potential to be a source of novel cytotoxic/antimicrobial compounds. This is the first report of diversity of fungal endophytes isolated from  M. citriodora .    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-017-0961-2) contains supplementary material, which is available to authorized users.

Diversity, Phylogeny, anticancer and antimicrobial potential of fungal endophytes associated with Monarda citriodora L.