Cyclopia subternata plants are traditionally used for the production of the South African herbal tea, honeybush, and recently as aqueous extracts for the food industry. A C. subternata aqueous extract and mangiferin (a major constituent) are known to have anti-diabetic properties. Variation in phenolic composition and antioxidant capacity is expected due to cultivation largely from seedlings, having implications for extract standardization and quality control. Aqueous extracts from 64 seedlings of the same age, cultivated under the same environmental conditions, were analyzed for individual compound content, total polyphenol (TP) content and total antioxidant capacity (TAC) in a number of assays. An HPLC method was developed and validated to allow quantification of xanthones (mangiferin, isomangiferin), flavanones (hesperidin, eriocitrin), a flavone (scolymoside), a benzophenone (iriflophenone-3-C-β-glucoside) and dihydrochalcones (phloretin-3',5'-di-C-β-glucoside, 3-hydroxyphloretin-3',5'-di-C-hexoside). Additional compounds were tentatively identified using mass spectrometric detection, with the presence of the 3-hydroxyphloretin-glycoside, an iriflophenone-di-O,C-hexoside, an eriodictyol-di-C-hexoside and vicenin-2 being demonstrated for the first time. Variability of the individual phenolic compound contents was generally higher than that of the TP content and TAC values. Among the phenolic compounds, scolymoside, hesperidin and iriflophenone-3-C-β-glucoside contents were the most variable. A combination of the measured parameters could be useful in product standardization by providing a basis for specifying minimum levels.