► Four Chinese pummelo cultivars and one grapefruit cultivar were collected. ► The flavonoid composition in flavedos and juices of samples were analysed. ► Twenty-eight flavonoids were identified. The flavonoid composition of flavedos and juices from four Chinese pummelo cultivars (Citrus grandis ‘Shatianyu’, C. grandis ‘Guanximiyu’, C. grandis ‘Yuhuanyu’, and C. grandis ‘Cuixiangtianyu’) and one grapefruit cultivar (Citrus paradisi ‘Changshanhuyu’), was investigated using high-performance liquid chromatography diode array detection electrospray ionisation mass spectrometry (HPLC-DAD-ESI MS/MS). Twenty-eight flavonoids were identified. Naringin was the predominant flavanone in these pummelo varieties, whereas naringin and neohesperidin were the principal flavanones found in C. paradisi ‘Changshanhuyu’. The four pummelo cultivars had higher levels of flavones when compared with the grapefruit. Based on the flavonoid profiles in flavedos and juices, four pummelo cultivars and one grapefruit cultivar were well separated.