Lake Baikal is the only freshwater reservoir inhabited by deep‐water fauna, which origi-nated mostly from shallow‐water ancestors. Ommatogammarus flavus and O. albinus are endemic scavenger amphipods (Amphipoda, Crustacea) dwelling in wide depth ranges of the lake covering over 1300 m. O. flavus had been previously collected close to the surface, while O. albinus has never been found above the depth of 47 m. Since O. albinus is a promising model species for various re-search, here we tested whether O. albinus is less metabolically adapted to atmospheric pressure than O. flavus. We analyzed a number of energy‐related traits (contents of glucose, glycogen and adenyl-ates, as well as lactate dehydrogenase activity) and oxidative stress markers (activities of antioxi-dant enzymes and levels of lipid peroxidation products) after sampling from different depths and after both species’ acclimation to atmospheric pressure. The analyses were repeated in two inde-pendent sampling campaigns. We found no consistent signs of metabolic disturbances or oxidative stress in both species right after lifting. Despite O. flavus surviving slightly better in laboratory con-ditions, during long‐term acclimation, both species showed comparable reactions without critical changes. Thus, the obtained data favor using O. albinus along with O. flavus for physiological research under laboratory conditions.