One interesting question in evolutionary biology is to understand how genome regulation contributes to environmental adaptation. Towards this goal we performed an experimental evolution by maintaining in vitro two clones of the fungal wheat pathogen Zymoseptoria tritici under fluctuating or stable temperatures for 50 weeks. Whole transcriptome of ancestors and evolved populations were assessed at the two stable temperatures used during the experimental evolution. Our results show a large effect of genetic background and temperature on the abundance of transcripts, with respectively 72 % and 9 % of the total phenotypic variance explained. A model based on a negative binomial distribution using read counts showed a strong response to the selection, with more than 2000 genes differentially expressed among the regimes (ancestral state, stable, fluctuating). However gene expression profiles in response to selection were very different between the two genetic backgrounds. Results from the first genetic background reveal 2.3 % of the genes (254 genes randomly distributed throughout the genome) were differentially expressed between stable and fluctuating selection. A co-expression analysis using gaussian mixture models revealed 3 large clusters, comprising 665 genes with a different expression profile between fluctuating selection and ancestral state, suggesting a transcriptome rewiring associated with fluctuations. Gene ontology enrichment analysis on these top-three clusters showed enrichment for cell division and cell wall biosynthesis categories, consistent with fluctuating selection having a role in these two biological processes. Within the second genetic background, we did not detect any genes with transcriptional profile change showing significant differences with their ancestral state and between stable and fluctuating selection. We observed that the 421 genes with similar transcriptionnal change for stable and fluctuating selection were enriched in GO terms related to cell cycle. Finally, an analysis on gene expression level plasticity in response to temperature revealed that more genes under fluctuations than genes under stable selection evolved towards a loss of plasticity when compared to their ancestors. These findings are consistent with models predicting that fluctuating selection can favor genetic canalization.