Endophytes which reside asymptomatically in living plant tissues are believed to produce the compounds similar to their host [1]. Due to the antimicrobial properties of Thymus, its endophytic fungi are expected to have these properties too. In the present research the antimicrobial effect of endophytes isolated from Thymus as well as their extract was investigated on several plant (Botrytis cinerea, Xanthomonas arboricola and Streptomyces scabies) and human (Escherichia coli ATTCC 25922 and Staphylococcus aureus ATTCC 33591) pathogens. The effect of endophytes on B. cinerea showed that the greatest inhibition percentage was related to M24 isolate (Fusarium subglutinans) (61.33%) but there was no statistically significant difference between this isolate and isolates M22, M15, M12 and M73 belonging to Fusarium genus and M75 isolate (Phoma). Out of 89 endophytic isolates, only three isolates M32, M35 and M33 (sterile mycelia) affected E. coli and nine isolates showed biocontrol effect on human pathogenic bacterium S.aureus with a significant difference at 1% level. M35 (with antibacterial potential 1.1) showed high activity on X. arboricola bacterium. In the case of S. scabies, all Fusarium isolates prevented from its growth. Among other isolates only M32 and M33, belonging to sterile mycelia, could affect the growth of this bacterium with a significant difference. The extracellular metabolites of endophytic fungi were used in 7 concentrations (0, 12, 48, 96 and 192 mg/ml) to control fungal and bacterial pathogens. The concentrations of 6, 12, 24, and 48 mg/ml had no effect on B. cinerea growth. In the concentration of 192 mg/ml, following the positive control, Fluconazole fungicide, M87 (Alternaria alternata) had the most effect on B. cinerea. In the concentration of 96 mg/ml, the extracts of M89 (F. lateritium), M32 (sterilemycelium), M29 (Fusarium sp.) and M24 (F. subglutinans) displayed inhibition halo. The concentrations of 6, 12, 24, 48 and 96 mg/ml had no effect
