The distribution and diversity of acidophilic microbe at the ore surface of Zijinshan commercial low-grade copper bioleaching heap operated at pH 0.8 were investigated. Samples taken from -1m, -2 m, -3m from the top of heap surface were investigated by 16S rRNA gene clone library. Phylogenetic analyses of 16S rRNA fragments revealed that the retrieved bacterial sequences mainly related to genus Acidithiobacillus (64.6%), genus Leptospirillum (27.3%), genus Sulfobacillus (3.1%) and genus Ferrimicrobium(1.6%). For archaea, only Ferroplasma acidiphilum was detected. Bacterial diversity in the heap was increased from surface layer to underground. The proportion of genus Leptospirillum was sharply reduced (from 48.5% to 5%) from higher depth to lower depth and reverse correlation of increased A.ferrooxidans (from 0.9% to 15%) and S. thermotolerans (from undetectable to 7%) were found in the heap. Sulfur oxidizers including A.albertensis, A.caldus and A.thiooxidans also vertically increased from higher depth to lower depth (from 50.5% to 80%). These results indicated that genus Acidithiobacillus especially sulfur oxidizers A.albertensis, A.caldus and A.thiooxidans may play very important roles in the commercial low-grade copper bioleaching heap.