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Peucedanum japonicum has long been a staple in East Asian cuisine. In the context of traditional medicine, various members of the Peucedanum genus have been investigated for potential medicinal properties. In laboratory settings, some compounds derived from this plant have shown antioxidant and anti-inflammatory properties—characteristics often associated with potential medicinal applications. This study aimed to determine which part of the P. japonicum plants cultivated on two Korean islands contains the most antioxidant compounds. This determination was made through assessments of total polyphenol content and total flavonoid content, coupled with evaluation of antioxidant activity via DPPH and ABTS assays. The results showed that the aerial parts contain a richer array of bioactive compounds and demonstrate superior antioxidant activity compared to their root counterparts in the plants from both islands. To characterize the phytochemicals underpinning this bioactivity, LC-MS/MS and HPLC analyses were carried out. These methods detected varying amounts of chlorogenic acid, peucedanol 7-O-glucoside, rutin, and peucedanol, with good separation and retention times. This study addresses the lack of research on the antioxidant activity of different parts of P. japonicum. The findings hold significance for traditional medicine, dietary supplements, and the development of functional foods. Understanding antioxidant distribution aids in the development of medicinal and nutritional applications, influences agricultural practices, and contributes to regional biodiversity-conservation efforts. The study’s geographical scope provides insights into how location impacts the concentration of bioactive compounds in plants. Overall, the results contribute valuable data for future research in plant biology, biochemistry, and related fields.