We studied the photophysiological responses to ultraviolet radiation (UVR) of two diatoms, isolated from different environmental niches. Both species showed the highest sensitivity to UV radiation under relatively low temperature, while they were less inhibited under moderately increased temperature. Under the highest temperature applied in this study, the benthic diatom Nitzschia sp. showed minimal sensitivity to UV radiation, while inhibition of the planktonic species, Skeletonema sp., increased further compared with that at the growth temperature. These photochemical responses were linked to values for the repair and damage processes within the cell; higher damage rates and lower repair rates were observed for Skeletonema sp. under suboptimal temperature, while for Nitzschia sp., repair rates increased and damage rates were stable within the applied temperature range. Our results suggested that the response of the microalgae to UV radiation correlated with their niche environments, the periodic exposure to extreme temperatures promoting the resistance of the benthic species to the combination of high temperature and UV radiation.