Advances in DNA sequencing technologies have promoted the use of genome information as a key component in most of biological studies. In the case of biomining microorganisms, partial and complete genome information has provided critical clues for unraveling their physiology. This information has also provided genetic material for the generation of functional and biodiversity directed markers. In this work, we present a compilation of the most relevant findings based on genomic analysis of the model organism Acidithiobacillus ferrooxidans ATCC23270 that were extended and compared to the recently sequenced genomes of Acithiobacillus thiooxidans and Acidithiobacillus caldus. The phylogenetic relatedness of these three microorganisms has permitted the identification of a shared genomic core that encodes the common metabolic and regulatory functions critical for survival and proliferation in extremely acidic environments. We also identified microorganism-specific genomic components that are predicted to be responsible for the metabolic speciation of these microorganisms. Finally, we evaluated the impact of lateral gene transfer on these genomes in order to determine the functional contribution of this phenomenon to the fitness of these microbial representatives. The information gathered by genomic analyses in the Acidithiobacillus genus will be presented in conjunction with other biomining genomic and metagenomic information in order to generate a more comprehensive picture of the biodiversity, metabolism and ecophysiology of the bioleaching niche.