Four samples were studied from four separated sites with heap leaching in the Yinshan Lead-Zinc Mine and the Dongxiang Copper Mine in Jiangxi province, China. The compositions and structures of archaeal communities in four sites were identified by a polymerase chain reaction-based cloning approach. A total of six operational taxonomic units (OTUs) was obtained from four samples. The highest percentage of overlapped OTUs was 88.9% between sites DX and D1. Phylogenetic analysis revealed that archaea in the four acid mineral bioleaching systems fell into two divisions: Thermoplasma and Ferroplasma. The proportions of Thermoplasma and Ferroplasma in all four sites were 20.6% and 79.4%, respectively. The proportions of clones clustered with Ferroplasma in four sites were 93.8% (D1), 30.5% (D3), 100% (DY), and 93.2% (DX), respectively. The proportions of clones clustered with Thermoplasma in the other three sites were 6.2% (D1), 69.5% (D3), and 6.8% (DX), respectively. The results of principal component analysis based on the percentages of six OTUs obtained from four sites and geochemical data from four sites suggested that the concentrations of elements such as lead, cobalt, and sulfur might be the reason causing the different archaeal structure in site D3 than those in the other three sites.