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With the financial protection of National Iranian Copper Industries Company, the composition of bacterial populations in Aliabad copper mine was investigated by electron microscopy and by analysis of DNA obtained from bacteria after ores laboratory cultures. This analysis consisted of the characterization of the spacer regions between the 16 and 23s genes in the bacterial rRNA genetic loci after PCR amplification. The size of the spacer region amplified from DNAs obtained from samples, were compared with the sizes of that obtained from culture of the bioleaching bacterial reference (Acidothiobacillus ferrooxidans DSMZ 583) and the 16s-23s intergenic spacer regions sequences in database. Further identification of the locale species was achieved by sequencing of the PCR product. The alignment result showed a great amount of similarity between the new bacteria and Thiobacillus ferrooxidans.