Bauhinia madagascariensis Desv. is a deciduous tree that is recently acclimatized in Egypt. Herein we report metabolites profile and asses antioxidant activity of Bauhinia madagascariensis Desv as compared to Bauhinia purpurea L. Secondary metabolites of B. madagascariensis and B. purpurea aerial parts methanol extracts were investigated using UPLC-ESI-QTOF-MS/MS. A total of 59 metabolites in B. madagascariensis and 66 metabolites in B. purpurea methanol extracts were identified. The identified classes in both extracts were flavonoids, phenolic, carboxylic and fatty acids, coumarins, stilbenes and acyclic diterpenoids. The most abundant class in both extracts was carboxylic acids. The total phenolic and flavonoid contents in B. madagascariensis and B. purpurea were 429.4 ± 4.17 mg (GAE)/g, 129 ± 1.83 mg (QE)/g and 353 ± 3.81 mg (GAE)/g, 72 ± 3.2 mg (QE)/g respectively, which reflects the richness of B. madagascariensis in total phenolic and flavonoid contents as compared to B. purpurea.. The antioxidant activity of the tested extracts has been evaluated using DPPH, H2O2 and FRAP antioxidant methods. B. madagascariensis extract showed stronger antioxidant capacity as compared to B. purpurea extract which could be assigned to the higher concentration of phenolic and flavonoid contents. The findings highlighted that B. madagascariensis is a good candidate for more studies against diseases originate from oxidative stress.