Ferredoxin/flavodoxin‐NADPH reductases (FPRs) catalyze the reversible electron transfer between NADPH and ferredoxin/flavodoxin. The Acinetobacter sp. Ver3 isolated from high‐altitude Andean lakes contains two isoenzymes, FPR1ver3 and FPR2ver3. Absorption spectra of these FPRs revealed typical features of flavoproteins, consistent with the use of FAD as a prosthetic group. Spectral differences indicate distinct electronic arrangements for the flavin in each enzyme. Steady‐state kinetic measurements show that the enzymes display catalytic efficiencies in the order of 1–6 μm−1·s−1, although FPR1ver3 exhibited higher kcat values compared to FPR2ver3. When flavodoxinver3 was used as a substrate, both reductases exhibited dissimilar behavior. Moreover, only FPR1ver3 is induced by oxidative stimuli, indicating that the polyextremophile Ver3 has evolved diverse strategies to cope with oxidative environments. Extremophilic microorganisms are an invaluable source of new biomolecules with unique characteristics. The genome of Acinetobacter sp. Ver3 isolated from high‐altitude Andean lakes encodes two ferredoxin/flavodoxin‐NADP+ oxidoreductases, FPR1ver3 and FPR2ver3, which display kinetic and spectroscopic characteristics similar to other prokaryotic FPRs and contribute to the bacterial protection against oxidative stress.