Thymus species are amongst the most popular medicinal plants because of their biological effects and pharmacological properties, and they are widely used in folk medicine for many disorders. Fourteen ecotypic Thymus kotschyanus essential oils were isolated, and the biological functionalities of ecotypic oils were characterized in terms of free radical scavenging and antigenotoxic properties. The most abundant ecotypic oil constituents were thymol and carvacrol (27.2–75.6%). The oils produced scavenging capacity, bleaching inhibitory capacity, and COMET‐inhibitory capacity values in a dose‐dependent manner ranging from 0.15 to 4.79 mg/ml, 0.04 to 3.1 mg/ml and 0.03 to 5.00 mg/ml, respectively. The benefits of T. kotschyanus essential oils from different regions vary, and they represent an inexpensive source of natural substances that have the potential to be used as antioxidative and antigenotoxic agents. Although the impacts of the microenvironment, climate difference and agronomical condition on the medical benefits of the plant were complex and highly context dependent, some correlations among the biological effects, main essential constituents, and the geographical environment were predicted. Copyright © 2016 John Wiley & Sons, Ltd.