The study was conceived to evaluate the difference in the chemical composition as well as the difference in the antimicrobial activities of the essential oils of Taxus media and Taxus chinensis var. mairei leaves. The chemical composition of essential oils which obtained by hydrodistillation method, were analysed by gas chromatography-mass spectrometry (GC-MS) system, and the relative amount of the chemical components of the essential oils were determined by the peak area normalization method. Remarkable differences were recorded between the percentages of a few constituents from the two essential oils. A total of 34 compounds were identified from the essential oil of Taxus media leaves, with the compounds of the dominant are Benzene propanenitrile (21.30%), 1, 4-Dioxane-2, 3-diol (20.13%), 3-Bromo-3-methyl-Butyric acid (17.92%) and 1-hydroxy-2-Butanone (9.85%). For the essential oil of Taxus chinensis var. Mairei leaves, 33 compounds were identified with the compounds of the dominant are Benzene propanenitrile (49.39%), 1-hydroxy-2-Butanone (12.72%), Acetic acid (5.39%), 1-octen-3-ol (4.28%) and (E)-3-(2-hydroxyphenyl)-2-Propenoic acid, (3.53 %). The ﬁlter paper disc agar diffusion method was used to test the antimicrobial activities of the essential oils, and diameter of antibacterial zones (DD) value and minimum inhibitory concentration (MIC) value were used to evaluate the antimicrobial activity. The result showed that the essential oil of Taxus media leaves possessed stronger antimicrobial activity than the essential oil of Taxus chinensis var. mairei leaves against the two tested bacteria.