Acid mine drainage (AMD) is a widespread problem in the Eastern United States. Several passive and active methods can be used as remediation strategies for the abandoned mine spoils. However, most are costly and/or unreliable. An alternative method is to take advantage of the biological oxidation of Fe(II) to Fe(III) by microorganisms (like acidophilic Fe-oxidizing bacteria indigenous to these sites), which may be a more reliable and less expensive means of removing Fe from AMD impacted sites. This study aims at understanding the activity of iron oxidizers along a sampling transect with contrasting rates of iron removal by assessing the Fe-oxidizing genes involved in the iron oxidizing pathway under low pH conditions. We have identified two iron oxidizing genes in Acidithiobacillus ferroxidansencoding rusticyanin (Rus) and Fe oxidase (Iro) for which we will assess using PCR and Q-PCR. We hypothesize that iro and rus genes can be detected in the contrasting treatment systems and their abundance reflects iron oxidation activity along a sampling transect. The gene iro is homologous to the high-redox potential iron-sulfur proteins (HiPIP), which serves as key electron acceptor for electron transduction pathways such as during the oxidation of Fe (II) to Fe (III). Because of the homology between iro to the HiPIP proteins, studies suggest that the iro gene is a new member of the HiPIP protein family. Rus is a blue copper protein thought to play a principal role in the electron transport pathway of Acidithiobacillus ferroxidans We designed specific primers for PCR, by aligning iro and rus gene sequences from GenBank homologues obtained from different strains of Acidithiobacillus ferroxidans. Using these primers we obtained amplicons of correct size from acid mine drainage samples, enrichment cultures and ATCC reference cultures. Q-PCR was used to compare frequency of genes as related to iron oxidizing activity.