Plants of the genus Monochoria have long been utilized in food, cosmetics, and traditional herbal treatment. Thailand has the highest species diversity of this genus and a new member, Monochoria angustifolia (G. X. Wang) Boonkerd & Tungmunnithum has been recently described. This plant is called “Siam Violet Pearl” as a common name or “ไข่มุกสีม่วงแห่งสยาม” as its vernacular name in the same meaning in Thai language. Despite their importance, few researches on Monochoria species have been conducted. This study, thus, provided the results to fill in this gap by: i) determining flavonoids phytochemical profiles of 25 natural populations of M. angustifolia covering the whole floristic regions in Thailand, and ii) determining antioxidant activity using various antioxidant assays to investigate the probable mechanism. The results revealed that M. angustifolia presented a higher flavonoid content than the outgroup, M. hastata. Our results also revealed that flavonoids might be used to investigate Monochoria evolutionary connections and for botanical authentication. The various antioxidant assays revealed that M. angustifolia extracts preferentially act through a hydrogen atom transfer antioxidant mechanism. Pearson correlation analysis indicated significant correlations emphasizing that the antioxidant capacity is most probably the result of a complex phytochemical combinations rather than of a single molecule. Altogether, these results showed that this new species provide an attractive alternative starting material with phytochemical variety and antioxidant potential for the phytopharmaceutical industry.