The main aim of this work is to provide new evidence regarding the interaction of chalcopyrite with an unknown thermophilic bacteria isolated from Rio Tinto mines (Huelva, Spain). This new microorganism gives very high copper recoveries (more than 80%) when a chalcopyrite concentrate is bioleached. Study of the solid massive samples after bioleaching by scanning electron microscopy (SEM) and non-dispersive X-ray microanalysis (EDS) confirmed its ability to attack ore. Chalcopyrite leached in the presence of this bacteria underwent a very strong superficial transformation in comparison with the sample attacked either in the absence of bacteria or in the presence of Fe3+. The attack started in cracks and genetic defects and finally reached the whole chalcopyrite surface. As a consequence of this, the ore showed deep cracks and a very rough surface. The presence of Fe2+ to increase the bacteria activity did not improve chalcopyrite bioleaching. These results were similar to those obtained in the absence of bacteria but in the presence of ferric ions. Therefore, the very good capacity of this new thermophilic microorganism for bacterial leaching and its advantages over conventional chemical leaching were demonstrated.