The Antimicrobial activity of the essential oils and their constituents against some microorganisms have been reported. Thymus is widely used in Libya folk medicine for its antimicrobial activity. Essential oils of thymus and their phytoconstituents have shown promising antimicrobial activity in vitro and in vivo. Therefore, the objective of this study was to evaluate antimicrobial activity of the essential oil (EO) of Thymus Capitatus against the yeast Candida albicans and the Gram negative bacteria Klebsilla pneumna. The essential oil from aerial parts of the plant was subjected to hydrodistillation, in order to extract Thymus volatile oil. Fourier transform infrared (FT-IR) spectroscopy was conducted to determine functional group of thyme volatile oil. The in vitro antimicrobial activity of thyme volatile oil was evaluated against Candida albicans and bacteria Klebsilla pneumna using agar disc diffusion method.. The data were subjected to ANOVA according to the SPSS 21 software. Results showed that percentage yield of thyme oil extract obtained was 5.67%. Thymol was the main components of thyme oil. According to the results, The inhibitory zone around the paper discs showed that thyme essential oil has the greatest effect against Candida albicans and Klebsilla pneumna . thyme oil displayed a large zones of inhibition against C. albicans and Klepsiella sp with 37mm and 33mm respectively. Whereas positive controls Nystatine, Tetracycline, Azithromycin and kanamycin displayed inhibition zones were 90, 10, 13 and 12 mm respectively. After performing controlled studies and experimenting with different types of antibiotics, thyme essential oil may can be used in treating Candida albicans and Klebsilla pneumna.