Zymoseptoria tritici causes Septoria leaf blotch (SLB), the most important foliar disease in winter wheat in Northern Europe and the UK. Chemical control of Z. tritici has seen a continuous introduction and substitution of fungicides with distinct mode of actions, due to the development of fungicide resistance. Emergence of diverse resistance mechanisms and their fixation in field populations of Z. tritici represents a constant threat to the control of SLB by fungicides. The aim of this research was to determine the biological potential of Z. tritici to adapt to the multi-site inhibitors chlorothalonil and folpet, and the single-site succinate dehydrogenase inhibitor (SDHI) fluxapyroxad. In vitro microtitre plate based fungicide sensitivity assays indicated that there was evidence for reduced sensitivity to chlorothalonil or folpet in the Z. tritici field isolates tested. Field isolates obtained from plots treated with solo applications of chlorothalonil or folpet were less sensitive to the fungicides compared with isolates sampled from non-treated plots. No evidence was found for reduced sensitivity to fluxapyroxad in the same set of field isolates. RNA sequencing analysis of the genome-wide transcriptional response of the reference Z. tritici isolate IPO323 after exposure to chlorothalonil or folpet in the lag and log phase of growth revealed a compound-specific “functional gene expression signature”. In addition, several genes encoding glutathione S-transferase (GST), ATP-binding cassette (ABC) or major facilitator superfamily (MFS) efflux pumps were significantly overexpressed in response to chlorothalonil or folpet exposure. In vitro evolutionary studies determined the course of evolution of resistance to the succinate dehydrogenase inhibitor (SDHI) fluxapyroxad in replicate populations of Z. tritici derived from the sensitive isolate IPO323. Resistance to fluxapyroxad arose mainly through alterations in the target protein that also often conferred cross-resistance to other SDHIs (e.g. fluopyram and carboxin). Additionally, overexpression of an ABC transporter or a GST gene was associated with resistance to fluxapyroxad and lower sensitivity to fluopyram or carboxin in a mutant without target-site alteration. The frequency of six amino acid substitutions in the target protein subunits sdhB, sdhC or sdhD – determined by SNP pyrosequencing assays – indicated that evolution of resistance was driven by a successive substitution of fitter mutants carrying distinct amino acid substitutions as selection at increasing concentrations of fluxapyroxad continued.