Zymoseptoria tritici is a fungal pathogen of wheat responsible for the septoria leaf blotch disease. This disease is a major concern in bread and durum wheats growing areas worldwide. It can be controlled by fungicide treatments and the use of resistant wheat cultivars. To date, 21 resistance genes and 89 QTLs for resistance to septoria leaf blotch have been mapped in bread wheat. Despite this large availability of resistant sources, it remains a challenge to improve the resistance levels of wheat elite cultivars because of the mostly quantitative nature of wheat-septoria interactions and of the very high level of genetic diversity within pathogen populations. Our objective is to understand the genetic architecture of pathogenicity in Z. tritici by identifying its determinants and revealing the specificity of their interaction with resistance determinants in wheat. We have undertaken a genome wide association mapping approach (GWAS) to identify pathogenicity genes in Z. tritici. A collection of more than 2000 isolates has been established in France. The genetic diversity has been characterized in this collection, and 109 isolates selected for resequencing and pathogenicity assays. In so doing, we obtained the virulence spectra of the 109 French isolates, revealing the efficiency of known resistance STB genes in France, and allowing to detect known and unknown STB genes present in French elite cultivars. Furthermore, combining the precision of our pathology assays, the selection of wheat genotypes well characterized for their resistance determinants, and the precision of GWAS in our Z. tritici population, we have identified several candidate avirulence genes interacting with known resistance genes in bread wheat. Thus far, the small secreted protein AvrStb6 is the first avirulence gene to be identified and functionally validated in this important wheat pathogen.