Brucea javanica (L.) Merr. is a member of Simaroubaceae which call as Makassar Fruit and having medicinal potency. In the last few years fungal endophytes have been detected in hundreds of plants including medicinal plants. The current study aimed to isolate and characterization of endophytic fungi from roots, stems, leaves and fruit of Makassar fruit B. javanica. A total of 4 (four) genera of endophytic fungi were identified, which Trichoderma sp. isolated from roots and stems, Fusarium sp and Penicillium sp from fruits and Aspergillus sp from leaves.