Understanding the molecular mechanisms of thermal adaptation is crucial to predict the impacts of global warming. However, there is still a lack of research on the effects of rising temperatures over time, and of studies involving different populations from the same species. The present study focuses on these two aspects, which have been shown to be of great importance in understanding how organisms cope and adapt to ongoing changes in their environment. This study investigates the impact of global warming on the gene expression patterns of Drosophila subobscura populations from two different latitudinal locations after 23 generations of thermal evolution. Our results indicate that transcriptomic changes due to selection are contingent on the genetic background of the populations, with the high-latitude population exhibiting more pronounced changes. We found an interplay between plasticity and selection, with the high latitude population showing fewer initial plastic genes and lower levels of adaptive plasticity, but a greater magnitude of change in both plastic and selective responses during evolution under warming conditions compared to its low latitude counterpart. A substantial proportion of the transcriptome was observed to be subject to selection, despite the lack of observable response at the higher level of organisation. The interplay between plasticity and selection may prove to be an essential component in shaping species' evolutionary responses to climate change. Furthermore, the value of conducting studies on multiple populations of the same species is emphasised, given the identification of differences between populations with different backgrounds in several contexts.