Dracocephalum kotschyi Boiss, of the Labiatae family, is an endemic and native herbaceous plant of Iran, where it is known as Badrandjboie-Dennaie and Zarrin-Giah[1]. It has been traditionally used as a folk medicine and an additive to improve the taste and scent of tea and yogurt. D. kotschyi is an important source of essential oils [2] and flavonoids such as xanthomicrol[3], calycopterin and cirsimaritin with anticancer properties. In this study we collected plant samples in 13 natural habitats to locate valuable accessions for domestication and breeding. Methanolic (80%) extract of leaves was used to quantify xanthomicrol, cirsimaritin, calycopterin, apigenin and rosmarinic acid, which were also identified and quantified by ESI-MS and HPLC-DAD methods. Plants collected from the central regions of Iran showed the highest levels of methylated flavonoids whereas the plants from the north of the country contained the most rosmarinic acid. Taken as a whole, our results show that flavonoid contents in D. kotschyi depend on environmental conditions; a semi-arid climate and high exposure of the plants to UV radiation leads to an accumulation of methoxy derivatives, while wet and cold conditions increase rosmarinic acid accumulation.