Salinity is an important driver of microalgal populations and traits, influencing habitat transitions over evolutionary timescales and adaptive potential to environmental change. Diatom Phaeodactylum tricornutum has distinctive strain-specific phenotypic responses to environmental drivers including salinity, a broad stress tolerance, comprehensive reference genome and rich history in environmental stressor research. These features make it an ideal model to characterise microalgal phenotypic and gene expression responses to salinity change. We grew three strains of P. tricornutum, two from hyposaline (PSU 5-6) conditions of the Baltic Sea, and one from the North Sea, at three experimental salinity levels (PSU 3.5, 5 and 35) for 174 days (approximately 56-108 generations), followed by a transplant experiment with incubation at all three experimental salinity levels until growth reached a stationary phase. Cultures were analysed for differences in gene expression and phenotypic traits. Results reveal high levels of variation in both phenotypic and transcriptomic responses of Phaeodactylum tricornutum strains to salinity. These were driven by interactions between their origin salinity and long-term salinity acclimation, which modify responses of this diatom to short-term salinity changes. Phenotypic traits were closely tied to differences in culture morphotypes, and stress the importance of morphological plasticity for diatom responses to salinity.