Flaxseed and fennel seeds are rich sources of different types of phenolics such as lignans, phenolic acids, flavonoids, phenylpropanoids, and tannins. The present study was carried out to develop and optimize a technique for isolation and quantification of secoisolariciresinol diglucoside (SDG) from flaxseed and Anethole from fennel seeds and to assess the antioxidant activities of flaxseed (Linum usitatisimum L.) and fennel seeds (Foeniculum vulgare Mill.) extracts. The percentage of extract in fennel seeds and flaxseed was 5.72 and 6.31 %, respectively. Using HPLC, the predominant constituent in fennel seed was determined to be anethole (11.30±0.25 mg/g) and in flaxseed, it was secoisolariciresinol diglucoside (SDG) (8.35±0.52 mg/g) compared to the respective standards solution. Using SPSS, the obtained data from each parameter were statistically analyzed. There are numerous biological and pharmacological effects of trans-anethole. For antioxidant activity, 2,2′-azinobis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) showed higher results with acetone (80%), with fennel seed and flaxseed is 7.28±0.17 and 8.29±0.23 mM TE/g. while FTC method it was maximum for distilled water extract of fennel seed (48.35±0.19%) and Flaxseed (65.09±0.72%) and by β-carotene bleaching method, water extract of fennel seed and flaxseed also showed maximum antioxidant activity i.e. 83.06±0.02% and 86.23±0.38%. Additionally, it is used as a masking agent in food products as a flavoring agent. According to the findings of this study, fennel seeds and flaxseed contain bioactive compounds that may assist in the treatment of a number of chronic diseases.