This study consisted of the physicochemical, phytochemical and antioxidant characterisation of two varieties of Hibiscus sabdariffa, to evaluate the influence of genetic and environmental factors on these parameters leading to an objective and rigorous classification of our extracts. To this end, calyxes and seeds of the red and white phenotypes were collected in Bobo-Dioulasso, Dano and Nouna respectively in December 2019 and 2020. Principal component analysis showed that physico-chemical and biochemical parameters could potentially be used to discriminate varieties. The calyxes of the sabdariffa variety showed the best physicochemical profile (total phenolics, flavonoids, ascorbic acid), pigments (anthocyanins, chlorophyll) and antioxidant activity (free radical scavenging and SOD activity) while the seeds showed the best carbohydrate, lipid and peroxidation inhibition content. In view of these results, the red phenotype has an interesting nutritional and therapeutic potential. It could therefore be interesting candidate in the pharmaceutical and food industries.