Siegesbeckia orientalis L. is an annual herb widely distributed throughout the world and has many medicinal properties. In Chinese traditional system, it is popularly known as Xi-Xian and used for its anti-inflammatory properties. In the present study, two cytotypes (diploid and tetraploid) have been investigated for their secondary metabolites. The different plant parts have been explored in terms of total phenolics, total flavonoids, DPPH radical scavenging acitivity and total antioxidant capacity. Out of different plant parts, leaves have the maximum amount of secondary metabolites and antioxidant potential. HPTLC technique has been applied to quantify six marker compounds in the two cytotypes. Tetraploid cytotype has been compared with diploid cytotype, which shows that tetraploid has the maximum amount of studied secondary metabolites with high antioxidant potential.