An understanding of the physiology and metabolic complexity of microbial consortia involved in metal solubilization is a prerequisite for the rational improvement of bioleaching technologies. Among the most challenging aspects that remain to be addressed is how aerobic acidophiles, especially Fe(II)-oxidizers, contend with the paradoxical hazards of iron overload and iron deficiency, each with deleterious consequences for growth. Homeostatic mechanisms regulating the acquisition, utilization/oxidation, storage and intracellular mobilization of cellular iron are deemed to be critical for fitness and survival of bioleaching microbes. In an attempt to contribute to the comprehensive understanding of the biology and ecology of the microbial communities in bioleaching econiches, we have used comparative genomics and other bioinformatic tools to reconstruct the iron management strategies in newly sequenced acidithiobacilli and other biomining genomes available in public databases. Species-specific genes have been identified with distinctive functional roles in iron management as well as genes shared by several species in biomining consortia. Their analysis contributes to our understanding of the general survival strategies in acidic and iron loaded environments and suggests functions for genes with currently unknown functions that might reveal novel aspects of iron response in acidophiles. Comprehensive examination of the occurrence and conservation of regulatory functions and regulatory sites also allowed the prediction of the metal regulatory networks for these biomining microbes.