In this study, the carotenoids produced by the extremophile microorganisms Halococcus morrhuae, Halobacterium salinarium and Thermus filiformis were separated and identified by high-performance liquid chromatography connected to a diode array detector and a tandem mass spectrometer. The in vitro scavenging capacity of the carotenoid extracts against radical and non-radical species was evaluated. In halophilic microorganisms, the following carotenoids were identified: bacterioruberin, bisanhydrobacterioruberin, trisanhydrobacterioruberin and their derivatives. In the thermophilic bacterium, the carotenoids all-trans-zeaxanthin, zeaxanthin monoglucoside, thermozeaxanthins and thermobiszeaxanthins were identified. The antioxidant capacities of the carotenoid extracts of H. morrhuae (trolox equivalent antioxidant capacity = 5.07 and IC(50) = 0.85 μg mL(-1)) and H. salinarium (trolox equivalent antioxidant capacity = 5.28 and IC(50) = 0.84 μg mL(-1)) were similar and higher than those of the bacterium T. filiformis (trolox equivalent antioxidant capacity = 2.87 and IC(50) = 2.41 μg mL(-1)). This difference is related to the presence of acyclic carotenoids with both large numbers of conjugated double bounds and of hydroxyl groups in the major carotenoid of the halophilic microorganisms.