The genus Casuarina encompasses species with promising ethnomedicinal relevance, yet their phytochemical composition remains underexplored in North Africa. This study presents a comparative evaluation of the phenolic and flavonoid compounds in different organs of Casuarina glauca (from Djerba) and Casuarina cunninghamiana (from Sfax), Tunisia. Aqueous extracts were obtained using maceration and ultrasound-assisted extraction (UAE) techniques, followed by high-performance liquid chromatography with diode-array detection (HPLC-DAD) for compound identification and quantification. Across both species, a total of 29 compounds were detected, including phenolic acids, flavonoids, and phenylethanoid glycosides. Catechin emerged as the predominant molecule, showing high concentrations particularly in C. glauca leaves and C. cunninghamiana flowers. Extraction technique and plant organ significantly influenced total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity. UAE extracts, especially from C. glauca leaves and C. cunninghamiana leaves, exhibited the highest antioxidant activities as confirmed by DPPH and FRAP assays. This work constitutes the first comparative report on Tunisian Casuarina species, demonstrating their potential as rich sources of natural antioxidants with prospective applications in complementary medicine, preventive therapies, biotechnology, and ethnopharmacology.