By March 2015, 161 genomes of acidophilic microorganisms had been published, including 126 permanent draft and closed genomes and 35 partial genomes reconstructed from metagenomic data, distributed between Archaea (71), Bacteria (86) and Eukarya (4). This provides a rich source of latent data that can be exploited for understanding the biology of this group of organisms and for advancing biotechnological applications. The genomic data are already yielding valuable insights into the genome architecture and cellular metabolism of acidophiles, allowing the construction of useful models to probe their evolution and ecophysiology both in naturally occurring acidic environments and in industrial operations such as in the biorecovery of metals. Introduction The advent of genomics and the possibility of genome-wide comparative and evolutionary analyses have revolutionized the field of microbiology. This is particularly true for studies on acidophiles where genomics have proven to be a rich source of information that, in many cases, has proven difficult to access via biochemical and genetic studies given difficulties in their culturing and manipulation. An early review of acidophile genomes focused on comparative genomics and provided a very useful overview of metabolic functions and evolution (Angelov and Liebl, 2007). Several other mini-reviews discussed the genomics of acidophiles but these have focused on microorganisms involved in the biological recovery of copper and other metals under acidic conditions (bioleaching and biooxidation; Chapter 16) (Bonnefoy and Holmes, 2012; Cardenas et al., 2010; Jerez, 2008; Holmes and Bonnefoy, 2007; Quatrini et al., 2007b; Valenzuela et al., 2006). More recent commentaries touched upon acidophile genomics in the context of iron oxidation (Altermann, 2014; Hedrich et al., 2011). The present chapter describes and updates the genomic information discussed in the above reviews and extends the knowledge to describe more recently published genomes from diverse acidic environments. The chapter does not cover metagenomics (Chapter 13), except in the instances where metagenomic data have been used to partially reconstruct acidophile genomes; nor are genomes of viruses or plasmids included (Chapter 12); also, it does not discuss functional genomic applications such as proteomics (Chapter 14) and transcriptomics. One of the ultimate goals of genome science is to predict the overall cellular organization from molecular to higher levels, eventually leading to useful models of interactions of microorganisms with their environment including other microbial co-inhabitants. This goal can be approached by systematic comparison of genomes of related organisms adapted to both similar and different environments, thereby identifying corresponding trends in genomic content.FONDECYTFONDECYT