[Objective] The influence of wild blueberry and anthocyanins extract on gut microbiota of high-fat diet-induced C57BL/6 mice was investigated. [Methods] The C57BL/6 mice were fed with high-fat diet and supplemented with blueberry or anthocyanins extract. Twenty-five germ-free mice were divided into five groups: normal chow diet (NCD), NCD+10 g/100 g blueberry (NCD+BB), high-fat diet (HFD), HFD+10 g/100 g blueberry (HFD+BB), HFD+20 mg/100 g anthocyanin (HFD+ACN). During the ten weeks, food intake, caloric intake and body weight were measured weekly, and dynamic changes of intestinal flora were monitored by DGGE. [Results] There was no significant difference in food intake among these five groups. Average caloric intake was higher in mice fed HFD+BB and HFD+ACN diets compared to the NCD+BB diets. Although body weight gain of mice fed with HFD+BB increased most obviously, no significant difference in body weight was observed between the groups at ten weeks. As the research went on, the diversity of intestinal microorganisms in HFD group, HFD+BB group and HFD+ACN group changed dramatically. The similarity coefficients of PCR-DGGE profile in intestinal flora between HFD+BB group and NCD group was lowest. However, as for HFD+ACN group and NCD group, the value is higher compared with HFD group and NCD group. The sequencing results of the dominant bands revealed that dietary supplemented with blueberry or anthocyanins extract can significantly reduce the number of obesity-associated Firmicutes. [Conclusion] Wild blueberry and anthocyanins extract can modify the structure of the intestinal microbiota, simultaneously protect against imbalanced intestinal microorganisms of the high-fat diet-induced mice, and ameliorate obesity and attenuate lipid accumulation potentially.