Chamaecyparis obtusa is a species of cypress native to central Japan and is rich in a variety of active pharmaceutical ingredients such as flavonoids and essential oils.Flavonoids are most commonly known for their antioxidant activity.Quercetin and myricetin have been shown to have anti-inflammatory and antioxidant properties and are being investigated for a wide range of potential health benefits.A new hybrid organic-inorganic monolithic cartridge (45 × 9.0 mm i.d.) was synthesized, and it was used as the selective sorbent for extraction and purification of quercetin and myricetin from Chamaecyparis obtusa.The material was evaluated first, and the chromatography analysis was operated on a C18 column (150 mm × 4.6 mm i.d.) with ultraviolet (UV) detection at 372 nm.Under the optimum condition, a good linearity was obtained, and it was successfully applied to the purification of quercetin and myricetin from Chamaecyparis obtusa.This method effectively removed the impurities and avoided tedious pretreatment, and it provided a fast, economic and effective method for assaying trace drugs from natural plants.