The amounts of substances together with nutritional and medicinal properties of fruits from Berberidaceae family vary between the plant species. Aluminum chloride colorimetric assay was used for flavonoids determination in 250 g of dried fruit. The Folin-Ciocalteau method was used to determine the total phenolic compound contents. The free radical-scavenging activity was examined by stable 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH) assay. The level of total phenol in different Berberis Ecotypes was 241.5 mg/g for Black berberis khorasanica, 296.8 mg/g for Black berberis bakhtiarica and 157.5 mg/g for Red berberis khorasanica. Furthermore, anti-radical activities (IC50) of these three Iranian Berberis species were 221.1, 58.38 and 123.2 μg/mL respectively. The level of flavonol in Black berberis khorasanica was approximately 2.42-fold higher than Black berberis bakhtiarica and 5.49-fold higher than Red berberis khorasanica. The content of flavonoids in Black berberis bakhtiarica was aproximately 2 times more than its level in Black berberis khorasanica and 3.55 times more than its level in Red berberis khorasanica. The highest amount of phenol and total phenols were observed in Black berberis bakhtiarica as its anti-radical activity was approximately 3.8 times more than Black berberis khorasanica and 2.1 times more than Red Berberis khorasanica. We showed high level of antioxidant compounds in Black berberis bakhtiarica. Considering the rate of elements and compounds in three Iranian Berberis ecotypes and based on their antioxidant and anti-radical effects, the berberis can be of benefit to oppose free radicals in the body.