Acidophilic iron-oxidizing microorganisms are important in both environmental and biotechnological applications. These microorganisms are known to accelerate the dissolution of sulfur minerals such as pyrite (FeS2), leading to the acid mine drainage generation, a serious pollution problem, that makes these microorganisms essential to the commercial processing of minerals and sulfur. In order to answer this question, the diversity of native acidophilic bacterial species isolated from an acid mine drainage site in Peru was evaluated. The samples were collected from Yanacocha mining (3000 m.a.s.l.) located in the North of Cajamarca region, Yanamina mining (4440 m.a.s.l.) located in the middle of Huancavelica region; finally, SPCC mining (2000 m.a.s.l.) located in the South of Moquegua region. We isolated 11 strains from which three were identified as Acidithiobacillus ferrooxidans, two as At. ferrivorans, two as At. ferridurans, three as Leptospirillum ferrooxidans and one as Acidiphilium sp. by comparative sequencing of PCRamplified 16S rRNA genes. Phylogenetic analysis of the 16S rRNA genes revealed that some of the strains isolated are closely related to other already known, but there are some with similarities lower than 95 percent. Our results provide the first study on the diversity of iron-oxidizing bacteria isolated from acid mine drainage in Peru.