Several species within the Acidithiobacillus (At.) genus can derive energy from oxidizing ferrous iron and sulfur. Two bacterial strains according to their 16S rRNA gene sequences closely related to At. ferridurans and At. ferrivorans were obtained from the industrial sulfide heap leaching process at Minera Escondida (SLH), named D2 and DM, respectively. We applied statistical and data mining analyses to the abundance of At. ferridurans D2 and At. ferrivorans DM taxa in the industrial process over 16 years of operation. In addition, we performed phylogenetic analysis and genome comparison of the type strains, as well as culturing approaches with representative isolates of At. ferridurans D2 and At. ferrivorans DM taxa to understand the differential phenotypic features. Throughout the 16 years, two main operational stages were identified based on the D2 and DM taxa predominance in solution samples. The better suitability of At. ferrivorans DM to grow in a wide range of temperature and in micro-oxic environments, and to oxidize S by reducing Fe(III) revealed through culturing approaches can, in a way, explain the taxa distribution in both operational stages. The isolate At. ferridurans D2 could be considered as a specialist in aerobic sulfur oxidation, while isolate At. ferrivorans DM is a specialist in iron oxidation. In addition, the results from ore samples occasionally obtained from the industrial heap suggest that At. ferridurans D2 abundance was more related to its abundance in the solution samples than At. ferrivorans DM was. This dynamic coincides with previously obtained results in in-lab cell-mineral attaching experiments with both strains. This information increases our knowledge the ecophysiology of Acidithiobacillus and of the importance of diverse physiological traits at industrial bioleaching scales.