In this study, five endophytic fungi belonging to the
Aspergillus
and
Alternaria
genera were isolated from
Lagopsis supina
. The antimicrobial activity of all fungal fermented extracts against
Staphylococcus
and
Fusarium graminearum
was tested using the cup-plate method. Among them,
Aspergillus ochraceus
XZC-1 showed the best activity and was subsequently selected for large-scale fermentation and bioactivity-directed separation of the secondary metabolites. Four compounds, including 2-methoxy-6-methyl-1,4-benzoquinone (1), 3,5-dihydroxytoluene (2), oleic acid (3), and penicillic acid (4) were discovered. Here, compounds
1
and
4
displayed anti-fungal activity against
F. graminearum
,
F. oxysporum
,
F. moniliforme
,
F. stratum
,
Botrytis cinerea
,
Magnaporthe oryzae
, and
Verticillium dahliae
with diverse MIC values (128–512 μg/ml), which were close to that of the positive control antifungal, actidione (64–128 μg/ml). Additionally, compounds
1
and
4
also exhibited moderate antibacterial activity against
S. aureus
,
Listeria monocytogenes
,
Escherichia coli
, and
Salmonella enterica
, with low MIC values (8–64 μg/ml). Moreover, compounds
1
and
4
displayed selective cytotoxicity against cancer cell lines as compared with the normal fibroblast cells. Therefore, this study proposes that the endophytic fungi from
L. supina
can potentially produce bioactive molecules to be used as lead compounds in drugs or agricultural antibiotics.