Endophytic fungi live inside plants as symbionts for at least one period of their life cycle. They play an important role in plant defence and could be promising sources of valuable natural bioactive products. The present study aimed to select endophytic fungi antagonistic to Microcyclus ulei, the agent of South American Leaf Blight (SALB) responsible for the weak development of rubber plantations in Latin America. Endophytic fungi were isolated from leaves of three cultivars (FX3864, CDC312, MDF180) of Hevea brasiliensis (the rubber tree) with distinct resistance levels to the attack by Microcyclus ulei. Leaf samples were collected from a 5,000 ha area of the Michelin plantations (Igrapiúna, Bahia, Brazil). A total of 435 colonies of endophytic fungi were isolated, purified, and preserved in sterilized distilled water. Lyophilized culture filtrates obtained from 88 fungal isolates, grown in liquid malt extract medium, were tested in vitro at concentrations of 50% and 12.5% for their inhibitory potential against the germination of M. ulei PMB26 conidia. Thirteen filtered cultures of endophytic fungi that presented inhibitory activity above 80% (at the concentration 12.5%) were characterized taxonomically by sequencing the ITS regions of rDNA, revealing the following taxa: Fusarium sp., Gibberella sp., Glomerella cingulata, Microsphaeropsis sp., Myrothecium sp., Pestalotiopsis sp. and Phomopsis sp. Three taxa were detected only in the resistant cultivars: Microsphaeropsis sp., and Pestalotiopsis sp. in MDF180, and Myrothecium sp. in CDC312. The present work constitutes the first study showing inhibitory activity of rubber tree endophytic fungi on Microcyclus ulei. These results provide an encouraging basis for the identification of new bioactive molecules for an effective control of South American leaf blight.