The genome of the extremely thermoacidophilic bioleaching microorganism Metallosphaera sedula was sequenced, in collaboration with the DOE Joint Genome Institute. The 2.1 Mb genome (46% G+C content) encodes 2258 predicted open reading frames (ORFs), and presents a very “Sulfolobus”-like picture, although M. sedula is differentiated physiologically from other Sulfolobus species with sequenced genomes (Sulfolobus solfataricus, Sulfolobus tokodaii, and Sulfolobus acidocaldarius) by its metal-mobilization capabilities. Genes and pathways relevant to M. sedula’s bioleaching capacity were identified through comparative genomics analysis with Sulfolobus species and known mesophilic bioleachers, such as Acidithiobacillus ferrooxidans and Ferroplasma acidarmanus. Specifically, the genetic bases for carbon fixation, iron and sulfur oxidation, metal tolerance, and adhesion processes were examined. The implications of insights gleaned from genome sequence analysis as they relate to M. sedula’s importance in biomining processes will be discussed, along with DNA microarray and genetic system tools in development for future research in this area.