Variation in chemical composition and biological activity of essential oils of medicinal plants may be observed due to the developmental stage of collected plant materials. In the present study, we compared the chemical compositions and antimicrobial activity of the essential oils from the aerial part of Thymus daenensis Celak. and Thymus fedtschenkoi Ronniger at different developmental stages. The highest essential oil content in both species was observed at the full flowering stage. The phenolic monoterpene thymol (71.9-73.9 %) and the monoterpene alcohol linalool (45.5-83.1 %) were the most abundant constituents at all phenological stages of T. daenensis and T. fedtschenkoi, respectively. All the essential oils possessed high antibacterial and antifungal activities against the microorganisms tested (Staphylococcus aureus, Bacillus cereus, Enterococcus faecium, Escherichia coli, Salmonella enteritidis, and Candida albicans), although of different degrees. The essential oils from T. fedtschenkoi appeared to be more active on almost all bacterial and fungal strains than that of T. daenensis (with MIC values of 1-16 mg/ml and 2-32 mg/ml, respectively). The effect of the plant phenological stage on the antimicrobial activity and constituents of T. fedtschenkoi essential oil was more pronounced than for T. daenensis. Interestingly, the antimicrobial effects of T. fedtschenkoi essential oil obtained at the seed set stage was noteworthy against all tested microorganisms, apart from the resistant E. faecium. Overall, this study highlighted the importance of the choice of the harvesting time to achieve the optimum of essential oil quality and quantity