In the present study, endophytic fungi have been isolated from various parts of the medicinal herb
Hypericum perforatum
(St. John’s Wort), which is known as a source of medically important metabolites. The isolated strains were cultured in liquid media and their ability to synthesize hypericin, the secondary metabolite of the host and its suspected precursor, emodin was tested analyzing the extracts of the fermentation broth and the mycelia. The HPLC-UV analysis of the chloroform/methanol extracts of the mycelia revealed that three isolates were able to produce emodin (SZMC 23771, 19.9 ng/mg; SZMC 23772, 20.8 ng/mg; SZMC 23769, 427.9 ng/mg) and one of them also could synthesize hypericin (SZMC 23769, 320.4 ng/mg). These results were also confirmed via UHPLC-HRMS technique both in full scan and MS/MS mode. The strains producing only emodin belong to the section
Alternata
of the genus
Alternaria
, while the isolate producing both metabolites was identified as
Epicoccum nigrum
. The mycelial extracts of
E
.
nigrum
and the
Alternaria
sp. SZMC 23772 showed higher inhibitory activities in the antimicrobial tests against the six selected bacteria compared to the hypericin and emodin standards in the applied concentration (100 μg/mL), while in case of the
Alternaria
sp. SZMC 23771 lower inhibition activities were observed on
Staphylococcus aureus
and
Streptomyces albus
than the pure compounds.