Endophytes are gaining worldwide recognition because of their potential use in biotechnology and as sources of novel bioactive compounds. A total of 27 fungal endophytes were isolated from the root, stem and leaves of two medicinal plants: Ocimum gratissimum (13) and Jatropha tanjorensis (14). Occurrence of endophyte species of the plants were Alternaria alternata and Aspergillus flavus (22.22% each), Nigrosa oryzae and Penicillium chryseogenum (14.81% each) and Penicillium oxalicum (11.11%). Cladosporium sphaerospernum (7.41%) was isolated from Ocimum gratissimum only and Rhizoctonia solani (7.41%) from Jatropha tanjorensis only. More endophytes were present in the roots and leaves than stems of the plants. Antibacterial screening of 10 mg/ml of fungal extracts on five test organisms (Staphylococcus aureus, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae), using the Agar Well Diffusion Method showed Alternaria alternata with inhibitory zones 20.5±0.15 mm – 32.7±0.58 mm; Penicillium chryseogenum (14.5±0.20 mm – 28.79±0.26 mm); Aspergillus flavus (18.7±0.10 mm – 24.7±0.10 mm) and Nigrosa oryzae (18.6±0.15 mm – 24.7±0.06 mm each), with their highest antibacterial activity on Staphylococcus aureus. Cladosporium sphaerospernum (20.9±0.20 mm – 30.0±0.06 mm) and Penicillium oxalicum (11.3±0.01 mm – 22.8±0.15 mm) were most inhibitory to Bacillus cereus. Rhizoctonia solani had the least zones of inhibition (8.20±0.20mm – 14.7±0.06 mm) and most inhibitory to E. coli and Pseudomonas aeruginosa. The antibacterial activities of the extracts were comparable to that of the standard drug, chloramphenicol (28.4±0.40mm – 36.0±0.12mm). With further research and standardization, these extracts could serve as alternatives to synthesized antibiotics.