Four anthocyanins, namely petunidin-3,5-O-diglucosides(L1), petuinidi-3-O-rutinoside(trans-p-coumaroyl)-5-O-glucosides(L2),cyanidin-3-O-(trans-p-coumaroyl)-diglucoside(N1), and pelargonidin -3-O-(trans-coumaroyl)-diglucoside (N2) have been obtained by preparative HPLC from Lycium ruthenicum Murray and Nitraria Tangutorum Bobr. The stability and antioxidant capacity of these four individual anthocyanins were carried out in this paper. For stability capacity examination, pH stability (pH 1, 3, 5, 7, 9, 11 and 13), photostability (exposed to light), and thermostability (5 degrees C and 35 degrees C) were systematically investigated. As for antioxidant capacity evaluation, DPPH radicals scavenging assay and ferric reducing antioxidant power (FRAP) assay were employed. The results showed that acidic solution tended to be favorable condition for all anthocyanins mentioned above. However, as the pH of solution increased, anthocyanins were becoming more unstable. In photostability and thermostability assays, the acylated anthocyanins behaved more stable than non-acylated anthocyanins. These results also indicated that the anthocyanins which had more powerful radical scavenging ability (DPPH) tended to possess stronger FRAP capacity. These data also indicated that the structures of aglycone and acyl group greatly affected the stability and antioxidant capacity of anthocyanins. Given the results obtained from our study, the high stability and antioxidant merits that the purified anthocyanins displayed made the two berries of Qinghai-Tibetan plateau become ideal resources of natural pigment.