The thermal degradation of cyanidin 3-(6''-malonyl) glucoside and cyanidin 3-glucoside, which are the two major anthocyanins in blood orange juice, have been investigated using the pH-differential method and RP-HPLC method, respectively. Similar results could be obtained when the degradation kinetics of cyanidin 3-glucoside were studied by either the HPLC method or the pH-differential method. However, contrary results were obtained in the case of cyanidin 3-(6''-malonyl) glucoside. The HPLC analysis indicated that cyanidin 3-(6''-malonyl) glucoside was labile to eliminate a malonyl moiety to form cyanidin 3-glucoside before disappearing during thermal treatment and showed a lower thermal stability than cyanidin 3-glucoside, whereas the result obtained by the pH-differential method actually reflected the content of both cyanidin 3-(6''-malonyl) glucoside and its degradation intermediate. This caused an overestimate of the stability of cyanidin 3-(6''-malonyl) glucoside.