In order to optimize anthocyanin purification process, we used the grains of five black rice varieties as materials and a single factor experiment design to investigate the effect of various factors of resin adsorption in the purification of black rice anthocyanin. The yields of purified anthocyanin of brown rice and husk in different varieties were compared. Then, the antioxidant activities of anthocyanin from different varieties were analyzed by 1,1diphenyl2picrylhydrazyl (DPPH) method. Finally, PCR was used to detect the key structural genes in anthocyanin synthesis pathway of black rice so that to clarify the yields and antioxidant characteristics of anthocyanin from brown rice and husk of five different black rice varieties and this will provide technical support for the development and utilization of anthocyanin in black rice. The results showed that: (1) the optimum purification condition for extracts of black rice anthocyanin was 4 h of static adsorption equilibrium, 1.5 h of the desorption time, 2.5 of pH, 30 ℃ of temperature, 70% ethanol of eluent. (2) The highest yield of anthocyanin in brown rice came from Fuheixiangnuo (213 μg/g), however, to husk from Guchengheinuo (226 μg/g). Meanwhile, Guchengheinuo possessed the highest total yield of anthocyanin, 432 μg/g. (3) The DPPH clearance rate of anthocyanin in brown rice was 65.1%, and it in husk was 73.7%. The DPPH free radical scavenging capacity per gram anthocyanin freezedried powder from brown rice and husk were equivalent to 3.694 mmol and 4.208 mmol vitamin E, respectively. The antioxidant capacity of anthocyanin from husk increased by 13.9% compared with that from brown rice. (4) In the identification of the five key structural genes of anthocyanin synthesis pathway for five black rice, it was found that there was no flavonoid3′hydrogenase gene (OsF3′H) in Aixuenuo. And its anthocyanin yield in rice husk was also the lowest (125 μg/g) compared to the other four varieties, and it is suggested that OsF3′H may be related to the anthocyanin content came husk of black rice.