Climate change is significantly impacting the structure and function of marine ecosystems world wide with implications for species distribution ranges. In coastal systems, climate change may also alter other abiotic factors such as salinity, which may decrease due increased glacial melting in the Arctic or precipitation in temperate regions. Despite the prime ecological importance of kelps (order Laminariales) which dominate rocky benthic ecosystems in temperate to polar regions, the acclimation mechanisms and transcriptomic responses remain understudied. Here, we investigate the physiological and transcriptomic responses in sporophytes of the sugar kelp, Saccharina latissima to salinity stress after acclimation to temperature and their nterrelationships. Juvenile sporophytes of a strain from Roscoff, France were pre-cultivated at 8°C and 30 PSU for three months. After seven days of acclimation to 0°C and 15°C, sporophytes were exposed to a low salinity treatment (20 PSU) for 24 h. We established a reference transcriptome from all reads obtained through Illumina HiSeq. A total of 205 363 transcripts were assembled containing 135 959 “Trinity’s genes”. Gene expression is mostly driven by salinity stress than by temperature. The highest number of regulated genes, in comparison to the control, was found in response to the treatment 0°C low salinity (3003), followed by 8°C low salinity (1491) and 15°C low salinity (1158). Moreover, only few genes (168) were found to be differentially expressed in all low salinity treatments, showing that the response to low salinity is modulated by temperature. Growth, photosynthetic efficiency and pigment content were also impacted by stress.