Varthemia candicans (Delile) Boiss., naturally grows in the Northwestern costal region of Egypt. The present study was conducted to evaluate the diversity of V. candicans secondary metabolites in two habitats during different seasons. Results showed that flavonoids, alkaloids, saponins, and phenolic compounds content attenuated their maximum value during spring in sand dune habitat, however, it reached a peak during summer in Wadi Habbes habitat. HPLC analysis of phenolic compounds from aerial parts showed two common phenolic compounds in both habitats, eight unique phenolic compounds in the plant growing in sand dune, and four phenolic compounds characteristic to Wadi Habbes plants. The high antioxidant activity of the plant was attributed to its high phenolic compounds content.