The present research reports on the selective dissolution of copper and iron from a Chilean molybdenite concentrate using mesophilic, moderate and extreme thermophilic culture bacteria. From the results obtained it is deduced that molybdenite is not attacked by any of the above mentioned microorganisms, whereas the attack of the copper-iron species is dependent on various experimental conditions: pH, potential, pulp density, or addition of silver as catalyst. Optimal copper-iron dissolution is obtained using extreme thermophilic microorganisms and low pulp density (2% w/v). Total selective dissolution of chalcopyrite is achieved which leads to a pure molybdenite concentrate being obtained.