Dracocephalum kotschyi Boiss. (Lamiaceae) is an aromatic and perennial herb endemic to Iran with interesting pharmacological and biological properties. The flavonoids luteolin-7-O-glucoside, apigenin-7-O-glucoside (cosmosiin), luteolin 3'-O-β-d-glucuronide, luteolin, apigenin, cirsimaritin, isokaempferide, penduletin, xanthomicrol, calycopterin and the polyphenol rosmarinic acid were identified among 13 natural populations of the plant by ESI-MS, LC-DAD and LC-DAD-ESI-MS. The plant extracts containing the identified compounds showed significant antioxidant activity, which was correlated with the flavonoid content. Additionally, leaf and stem size and geographical variability among the studied populations were correlated with flavonoid accumulation. Canonical correlation analysis was used to find a relationship between plant dimensions and phytochemical composition, and the plants with the lowest growth indices were found to have the highest levels of methoxylated flavonoids.