The aim of this study was to quantitatively evaluate the phytochemicals, total phenol, flavonoids content and antioxidant activity in seed, leaf and bark of Zanthoxylum armatum. Antioxidant activities were examined by four different methods viz. DPPH, FRAP, metal chelating assay and superoxide scavenging assay.Significant correlations obtained indicated that phenols and flavonoids were the chief performers of antioxidant activity which proves Z. armatum is a potential source of useful natural antioxidants. The genetic variability among individuals of Zanthoxylum armatum from Uttarakhand, India was examined by using random amplified polymorphic DNA (RAPD). Leaf samples were collected from natural populations of three different regions of Uttarakhand i.e. Pithoragarh, Nainital and Almora. A total of 20 primers were tested on the DNA extracted from the 36 leaf samples, out of which 12 primers produced reproducible amplification products that were selected for PCR amplification. The results exhibited high genetic diversity in Z. armatum.