Detection of shiikuwasha (Citrus depressa Hayata) juice adulterated with calamondin (Citrus madurensis Lour.) juice was investigated by the analyses of (1) phloretin dihydrochalcone glucoside, 3',5'-di-C-beta-glucopyranosylphloretin (PD) detected by thin-layer chromatography and high-performance liquid chromatography (HPLC), (2) polymethoxylated flavones (PMFs), included nobiletin, tangeretin, and sinensetin, detected by HPLC, and (3) gamma-terpinene peak percentage obtained by headspace solid-phase microextraction gas chromatography with cryofocusing. PD was detected in calamondin juice (25.5 mg/100 mL) but not in shiikuwasha juice. Shiikuwasha juice contained higher levels of nobiletin (48.8 mg/100 mL) than calamondin juice (2.4 mg/100 mL). Shiikuwasha juice was characterized by containing a higher percentage of gamma-terpinene (12.3%) than calamondin juice (0.7%). A discrimination function obtained by a linear discriminant analysis with PMFs and a peak ratio of [nobiletin/tangeretin] and ?-terpinene detected the adulteration with accuracies of 91.7%. These three chemical markers were useful to detect shiikuwasha juice that is suspected of being adulterated with calamondin juice.