Small regulatory RNAs (srRNAs) control gene expression in Bacteria, usually at the post-transcriptional level, by acting as antisense RNAs that bind targeted mRNAs or by interacting with regulatory proteins. srRNAs are involved in the regulation of a large variety of processes such as plasmid replication, transposition and global genetic circuits that respond to environmental changes. Since their discovery a few years ago, it has become apparent that they are prolific and widespread. In this study, we describe bioinformatic approaches to srRNA discovery in the biomining microorganisms Acidithiobacillus ferrooxidans, A. caldus and A. thiooxidans. Intergenic regions of the annotated genomes were extracted and computationally searched for srRNAs. Candidate srRNAs that were associated with predicted sigma 70 promoters and/or rho-independent terminators were chosen for further study. The resulting potential srRNAs include known examples from other microorganisms and some novel candidates and reveal interesting underlying biology of the Acidithiobacillus genus.