Characterization of anthocyanins and flavonols and radical scavenging activity assays of extracts from four Chinese bayberry (Myrica rubra) varieties with different fruit colors were carried out. One dominant anthocyanin and three major flavonols were isolated by HPLC, and cyanidin-3-O-glucoside and two of three flavonols, myricetin and quercetin-3-O-rutinoside, were identified by cochromatography with authentic standards. Both DPPH* and ABTS*(+) cation assays indicated that the black varieties (Biji and Hunan) demonstrated much higher radical scavenging activities than the pink (Fenhong) and yellow (Shuijing) varieties, which may be attributed to much higher levels of anthocyanins, flavonoids, and total phenolics in the black varieties. Biji and Hunan had 6.49 and 6.52 mM Trolox equivalent antioxidant capacity (TEAC) per 100 g of fresh weight, whereas the pink (Fenhong) and yellow (Shuijing) bayberries had 1.32 and 1.31 mM TEAC/100 g. Different fruit color was reflected by the surface color and pigment extract color. Color stability of the pigment was dependent on pH, and the pigment was more stable at low pH (pH approximately 1.5). The lightness (L) increased while the chroma (C value) decreased with increase of pH until pH 5, but higher pH caused a small decrease for L and an increase for C.