Marine macroalgae are key organisms in polar coastal ecosystems. Brown macroalgae dominate rocky shores in both polar hemispheres, where they form huge kelp beds, which are habitat and feeding ground for diverse organisms. To compare physiological response of Arctic vs. Antarctic habitat structuring brown algae to different abiotic factors, Saccharina latissima (Kongsfjorden, Arctic) and Desmarestia anceps (Potter Cove, Antarctic) were exposed for 8h to 12 combinations of photosynthetically active radiation (PAR), UV radiation (UVR) and temperature. The data provide basis information on short abiotic stress in S. latissima and D. anceps. Temperature alone did not cause changes in photosynthetic efficiency, while UVR and high PAR decreased the maximum quantum yield of PS II down to 30% of the initial values. The endemic species D. anceps showed mostly similar responses to the applied stress treatments compared to the generalist S. latissima, indicating a certain tolerance of D. anceps to short periods of UVR and temperature stress. More data are needed to predict biological effects and ecological implications of changing abiotic factors, future studies should include several stress exposure times and gradual changing abiotic factors.