Endophytes of medicinal plants have the capacity to synthesis same or similar active substances with their hosts. To investigate the diversity and capacity to produce saponins of endophytic fungi of Panax ginseng, thirty-eight strains of were isolated. Polymerase chain reaction (PCR) and sequencing were used to identify the isolates, and saponins concentrations in the cultures were measured. Agar diffusion method was used to test antimicrobial activity. High-performance liquid chromatography (HPLC) was used to analyze ginsenosides produced by representative strains. Nectria, Aspergillus, Fusarium, Verticillium, Engyodontium, Plectosphaerella, Penicillium, Cladosporium, and Ascomycete species were isolated. Overall, 18.4% of the isolates belonged to Nectria (Nectria haematococca), 13.2% belonged to Aspergillus, and 10.5% belonged to Penicillium. The highest concentration of triterpenoid saponin was 0.181 mg/ml (Pg27), followed by 0.144 mg/ml (Pg30 and Pg42-1). According to the results of the phylogenetic results, these isolates were species of Fusarium, Aspergillus and Verticillium, respectively. The culture filtrate of Pg30 exhibited its antibacterial activity Staphylococcus aureus. Pg 27 and Pg30 could excrete the substances to inhibit the growth of Rhizoctonia solani. Pg42-1 showed strong inhibition against Klebsiella pneumoniae. From HPLC results, the ginsenoside Rb2 was detected in both Pg27 and Pg30 cultures. The ginsenoside Rc was found in Pg42-1 cultures. In conclusion, thirty-eight endophytic fungal strains were isolated and Pg27 (Fusarium sp.) has a potential application value in saponins production.