In Cu-Mo deposits it is usual to find considerable amounts of pyrite (FeS2). When processing this kind of ore by flotation, pyrite is rejected using lime to increase the pH to alkaline conditions (pH similar to 10-12). In the case of using seawater without pre-processing (raw seawater), the lime consumption increases dramatically and the recovery of molybdenite drops due to the precipitation of secondary ions (e.g. magnesium, sulfate, calcium and bicarbonate) on its surface. In order to avoid these negative effects, alternative ways of depressing pyrite should be considered. The current work introduces the use of Acidithiobacillus ferrooxidans, bacteria commonly used in bioleaching, as an alternative to depress pyrite in seawater flotation. This work presents the results of biodepression, at microflotation scale, in three systems: fresh water, saline water (35 g/l of NaCl, which corresponds to the salt concentration in seawater) and seawater. It was determined that when pyrite is bio-conditioned with A. ferrooxidans before flotation, recovery of pyrite at pH 8 drops from 99% to 24% and 34% in fresh water and saline water, respectively. A similar behavior is observed when running the experiments in seawater, where recoveries drop from 97% to 36% in the presence of A. ferrooxidans in flotation at natural pH (7.8-8.2). Results show that it is possible to bio-depress pyrite with A. ferrooxidans in seawater flotation at natural pH.