The exploration of microbial diversity in extremely acidic habitats has provided a vital base for the progression of minerals biotechnology. Three indigenous iron-oxidizing acidophilic bacterial strains were isolated through serial dilution of enriched bacterial culture from Baiyin Copper Mine Stope, China. The morphological, biochemical, physiological, and phylogenetic characteristics of isolates were investigated. These isolates were motile, Gram-negative, and curved shape with pleomorphism except isolate WG101 that was a straight rod. The optimum growth pH and temperature for all isolates were 1.5 and 30 °C, respectively, and showed extreme acidophilic nature. All the isolates showed obligate chemoautotrophic nature and used ferrous iron and pyrite as an energy source, however, isolates WG102 and WG103 were unable to use sulfur, while isolate WG101 could use elemental sulfur and reduced inorganic sodium thiosulfate as an energy source. The phylogenetic analyses based on 16S rRNA sequences revealed that the isolates WG101, WG102, and WG103 were homologous with Acidithiobacillus ferrooxidans strain AS2 (99%), Leptospirillum ferriphilum strain YSK (98%), and Leptospirillum ferrooxidans strain L15 (98%), respectively. These bacterial isolates showed efficient copper and zinc dissolution from the ore. The metals dissolution rate of At. ferrooxidans strain WG101 was 54.5 ± 4.33% (copper) and 49.6 ± 5% (zinc). The metals recovery rate of L. ferriphilum strain WG102 was 45.7 ± 3.5% (copper) and 40.5 ± 2.5% (zinc). The recovery rate of copper and zinc was 49.6 ± 4% and 46.5 ± 3% respectively in the case of L. ferrooxidans strain WG103. The findings of this study are consistent with the notion that the indigenous bacteria are more efficient in minerals dissolution.