By using culture-independent 16S rDNA based on cloning approach- restriction fragment length polymorphism (RFLP) analysis method, the composition of microbial communities in three bacterial culture samples, which were waste mining water obtained from Dexing Copper Mine, Jiangxi Province, China, enriched in different culture mediums, was determined. These bacterial samples were used to leach a complex copper-bearing sulfide. The 9K-I bacterial culture, was mainly composed of At. ferrooxidans and Leptospirillum species (group I, group II and group III), for 40 days' bioleaching, it had the maximum extraction efficiency of iron and copper, in the liquid, the concentration of Fe reached to 1450 mg/L, for Cu, it reached to 310 mg/L; The A-Y-I bacterial culture, was mainly composed of Acidiphilium sp. XTS-1 and Leptospirillum species (group II and group III), had the minimum extraction efficiency of iron (630 mg/L in liquid) and copper (81 mg/L in liquid). At. ferrooxidans and Leptospirillum ferrooxidans (group I) seemed to be bacteria playing important roles in extraction of copper and iron, in this study. Scanning electrode microscopy (SEM) results showed different species of bacteria had different abilities adsorbing on ore powder surface. The amount of bacteria adsorbed on ore powder surface may relate to the extraction efficiency of copper and iron from the complex copper-bearing sulfide.