Endophytes from medicinal plants have been demonstrated to produce bioactive chemicals with antibacterial capabilities. Previous research found many endophytes in Javanese ginseng roots. Identifying and comprehending the benefits of endophyte microorganisms is critical for boosting plant growth and defense. The aim of this study was to identify endophytic microbes from Javanese ginseng with antifungal activity. In this present study, two isolates the GJ-9 and FN-1, were analyzed using NL1/NL4 and ITS1/4 primers. The amplification and sequencing of the ITS and the D1-D2 LSU rRNA gene were performed. The D1-D2 LSU rRNA sequence analysis results showed that GJ-9 has similarities with Candida Spencermartinsiae with 99.82% percentage identity, while FN-1 has been identified as Aspergillus flavus according to the ITS sequence analysis result with 99.83% percentage identity. Antagonistic assays showed both isolates displayed considerable antagonistic ability against Rhizopus stolonifera, Pythium sp., Botrytis sp., and Fusarium sp, with overall inhibition rate were over 50%. The Aspergillus flavus showed the better ability to inhibit the growth of Phytium sp.(74.90%) and Rhizopus stolonifera (60%), while the Candida Spencermartinsiae is better for controlling Botrytis sp.(55.68%) and Fusarium sp.(60.39%). The result suggests the endophyte from Javanese ginseng can be used as an agent for controlling various plant diseases; furthermore, it could lead to a reduction of agrochemical inputs.