The polymethoxyflavonoids nobiletin and tangeretin are isolated from peels of shekwasha (Citrus depressa Hayata) and ponkan (Citrus reticulata Blanco). These natural products possess biological activities, including anticancer and anti-inflammation properties. This report describes an efficient method for the extraction and isolation of nobiletin and tangeretin from citrus peels using 1-ethyl-3-methylimidazolium methylphosphonate ([C 2 mim][(MeO)(H)PO 2 ]) and centrifugation/decantation. The results showed that the extraction yield of nobiletin and tangeretin using [C 2 mim][(MeO)(H)PO 2 ]/organic solvent (1:1 w/w) was 1.4 to 1.6 times higher than that using organic solvent. This extraction method is expected to be applicable for obtaining other organic compounds from natural sources.