Septoria tritici blotch (STB) caused by the ascomycete fungus Zymoseptoria tritici is currently one of the most devastating foliar diseases on wheat crops globally. STB is a major concern among European wheat producers, especially in humid, temperate areas, such as North-western Europe. Management of STB in Europe still relies heavily on use of fungicides and due to the intensive chemical control, pathogen populations started to evolve rapidly for resistance to fungicides. Wheat varieties with higher and durable resistance can provide an effective control to disease severity, but so far, cultivars with those resistance are not available. The aim of this investigation was to identify candidate genes for STB resistance during different infection symptom/stages (chlorosis, necrosis and pycnidia) by combining both QTL and transcriptomics analysis in a bi-parental doubled haploid winter wheat population. Based on the results, four QTLs were identified for STB resistance, of which, two were mapped for chlorosis, necrosis and pycnidia and the other two were only associated with necrosis and pycnidia. Transcriptome analysis of resistant and susceptible lines at 10 and 12 days after infection revealed up-regulation of 1,019 and 571 genes and down-regulation of 875 and 984 genes, respectively between the resistant and susceptible lines at each time point. The gene ontology analysis of the differentially expressed genes revealed that the top affected molecular functions at 10 dpi were sucrose-phosphate phosphatase activity, chitinase activity and oxidoreductase activity and at 12 dpi were ADP binding, ammonia-lyase activity. These results will be presented and discussed.