A strategy for the monitoring and control of genetic expression in an industrial bioleaching process of copper sulphide minerals is developed in order to understand more fully this process and investigate optimization possibilities. The aim of this research is to find a group of housekeeping genes to normalize the genetic expression data associated to the metabolic functions from industrial bioleaching samples obtained through specific real-time PCR. The data includes the quantification of the previously identified genes in the industrial process in samples from different strips (heap sections) and times. Two studies were carried out, one with the gene expression data associated to each species and the other with the expression data from all the genes detected in the industrial process, during a period of 18 months, using the VBA applet geNorm [1]. The first analysis showed that for the archaea Ferroplasma acidiphilum, the gene with the most stable expression codifies to the ribosomal protein S4 (rpS4) and secondly the mercury reductase gene (merA). In the case of Acidithiobacillus ferrooxidans DM and D2 strains, genes merA and pyruvate dehydrogenase (pdhA) presented similar factors of stability. In the community analysis it was concluded that the gene with the most stable expression was pdhA of A.ferrooxidans. A new analysis was done including other genes using geNorm to define the most stable genes for the whole community. In the community analysis it was concluded that the gene with the most stable expression was pdhA of A.ferrooxidans and merA of F.acidiphilum. © (2009) Trans Tech Publications.