Endophytes are important resources of bioactive compounds and due to their potential for secondary metabolites production, they are regarded as a potential reservoir of biotechnological applications. In this study, the bioactivity of bacteria and yeasts endophytes residing in Thymus sp. was evaluated. During April to October 2011, symptomless and healthy tissues of Thymus sp. were collected. A total of 23 strains of endophytic bacteria and 6 yeasts were isolated. The bio-effects of the endophytes were studied on Botrytis cinerea and plant pathogenic bacteria Xanthomonas arboricola pv. juglandis and Streptomyces scabies and human pathogens Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC. Growth inhibition mechanisms of the endophytes against B. cinerea were evaluated and it seems that the antimicrobial effects of bacterial endophytes are related to the production of protease enzyme, hydrogen cyanide and volatile compounds. Bacterial strains were identified as Bacillus, Pseudomonas and Xanthomonas of which Bacillus was the predominant isolate. For the first time, Bacillus is reported from Thymus eriocalyx, T. lancifolius, T. fallax, T. kotschyanus and T. vulgaris and Pseudomonas and Xanthomonas as endophytic bacteria from Thymus
