A total amount of 116 fungal strains, belonging to 30 genera, were acquired from the rhizosphere soil and plant of
Galinsoga parviflora
. A strain SYPF 7336, isolated from the rhizospheric soil, was identified as
Seltsamia galinsogisoli
sp. nov., by morphological and molecular analyses, which displayed high antibacterial activity. In order to study the secondary metabolites of
Seltsamia galinsogisoli
sp. nov., nine compounds were successfully seperated from the strain fermentation broth, including two new compounds and seven known compounds. Their structures were elucidated based on spectral analysis including 1D and 2D NMR. All the seperated compounds were evaluated for their antimicrobial activities. Compounds
2, 5
and
1
displayed antimicrobial activities against
Staphylococcus aureus
with MIC values of 25, 32 and 75 μg/mL, respectively. Moreover, morphological observation showed the coccoid cells of
S. aureus
to be swollen to a volume of 1.4 to 1.7-fold after treatment with compounds
1
,
2
and
5
, respectively. Molecular docking was carried out to investigate interactions of filamentous temperature-sensitive protein Z (FtsZ) with compounds
1
,
2
and
5
.