Native medicinal plants have been traditionally used to treat various bacterial infections, fungal infections, cancers, viral infections and cardiovascular diseases. Endophytes residing inside medicinal plants are capable of producing therapeutically important bioactive compounds. The study aimed to evaluate the antimicrobial activity of endophytic crude extracts against clinical isolates of Staphylococcus aureus and Escherichia coli. Acetone, methanol and ethyl acetate were used to extract the endophytic compounds. Acetone, methanol and ethyl acetate extracts from 24 endophytes were evaluated for antimicrobial efficacy against E. coli and S. aureus by agar well diffusion assay. Amplification of 16 S rRNA gene was used to confirm that the endophytes were bacteria. Whereas, M13 RAPDs were used to differentiate the endophytic bacteria, respectively. The antagonistic test was used to evaluate the interspecies interaction of endophytes in a single Petri dish. Qualitative thin-layer chromatography was used to identify the compounds present in the ethyl acetate crude extract. The 16 S rRNA PCR amplicons confirmed that nine of the most prolific endophytes are bacteria. M13 RAPDs analysis indicated that the endophytic bacteria are not the same. Endophytic acetone extracts from sample 1, 3, 9 and 17 exhibited the most potent antimicrobial efficacy against E. coli and S. aureus. Terpenoids, flavonoids and stilbenes were observed by the thin-layer chromatography charring profile. In this study, the endophytic crude extracts proved to possess compounds with antimicrobial activity against clinically important pathogens.