Although Thiobacillus ferrooxidans and Leptospirillum ferrooxidans are widely considered to be the microorganisms that control the rate of generation of acid mine drainage, little is known about their natural distribution and abundance. Fluorescence in situ hybridization studies showed that at Iron Mountain, California, T. ferrooxidans occurs in peripheral slime-based communities (at pH over 1.3 and temperature under 30 degreesC) but not in important subsurface acid-forming environments (pH 0.3 to 0.7, temperature 30 degrees to 50 degreesC). Leptospirillum ferrooxidans is abundant in slimes and as a planktonic organism in environments with lower pH. Thiobacillus ferrooxidans affects the precipitation of ferric iron solids but plays a limited role in acid generation, and neither species controls direct catalysis at low pH at this site.