Endophytic parasites are found in plant tissues. They colonize host plant tissues inter- and intracellular spaces without causing disease. They have a mutually beneficial relationship. Endophytic fungi were isolated from healthy plant of Heliotropism indicum, a medicinal plant found in India which is used in folk medicine. Among five endophytic fungi isolated, the fungal isolates showed activity against two tested phytopathogens (Xanthomonas sp) in preliminary screening, and the best results were obtained with Aspergillus sp (EF9). After fermentation in liquid media, the Aspergillus sp (EF9) demonstrated antibacterial activity in Potato Dextrose Broth. In the next step, ethyl acetate extract from the supernatant of broth culture were prepared and both exhibited antibacterial activity against phytopathogens (Xanthomonas sp). The best result was observed with 70 mg/mL. This study is the first report about the antibacterial activity of endophytic fungi residing in H. indicum roots, in which the fungus Aspergillus sp (EF9) demonstrated the ability to produce bioactive agents with antibacterial potential, and may provide a new lead in the pursuit of new biological sources of drug candidates in agricultural industry