In the present study, we have identified pelargonidin 3-glucoside, along with two known anthocyanin; cyanidin 3-sophoroside and cyanidin 3-glucoside, from acidified, methanolic extract of mangosteen pericarp. The compounds were separated by preparative HPLC after purification by partition against ethyl acetate and Amberlite XAD-7. The structures of the compounds were confirmed by high performance liquid chromatography (HPLC), UV–Vis absorption spectra, high-resolution electrospray mass spectrometry and 1D, 2D nuclear magnetic resonance (NMR) spectroscopy. This new pigment family adds to the growing body of data supporting the use of natural colourants in food. Cyanidin 3-sophoroside was the major anthocyanin detected in large amount (76.1%), followed by cyanidin 3-glucoside (13.4%) and pelargonidin 3-glucoside (6.2%).