The septoria leaf blotch disease is caused by the ascomycete fungus Zymoseptoria tritici. Nowadays, it is one of the most damaging diseases to wheats and triticale cultures in many regions of the world. The interaction between wheat and Z. trititi is complex because of its highly polygenic and mostly quantitative nature. Nevertheless, several wheat resistance genes, called Stb genes, correspond to the description of major resistance genes, i.e. qualitative phenotypic effect and involved in a gene-for-gene interaction with the fungus. So far, twenty-one qualitative Stb genes have been mapped in bread wheat. AvrStb6 was the first gene identified that confers avirulence to wheat cultivars carrying a known Stbgene, Stb6. Here, we report the cloning of AvrStb9 conferring avirulence to wheat cultivars carrying Stb9. AvrStb9 was identified by GWAS with Z. tritici isolates pathotyped on cultivar Soissons. The isolate IPO-09593 is avirulent while the reference isolate IPO-323 is virulent on Soissons. Replacement of the virulent allele with the AvrStb9 allele from IPO-09593 conferred an avirulence phenotype to transformed IPO-323 strains. Moreover, different recombination events in the AvrStb9 gene among the IPO-323 transformants allowed us to identify the protein domains involved in virulence. AvrStb9 encodes a large potentially secreted protein of unknown function. It is expressed in planta during the transition from the asymptomic to the necrotrophic phases of infection. The resistance Stb9 was first reported in cultivars Courtot and Tonic. We identified Stb9 following a genome-wide association study (GWAS) on elite bread wheat cultivars, and confirmed its presence in Soissons by QTL mapping in a population Beaver/Soissons. The genefor-gene relationship between AvrStb9 and Stb9 was shown by phenotyping Z. tritici transformants with either the virulent or the avirulent allele of AvrStb9 on near-isogenic lines carrying the resistant or susceptible allele at Stb9 in Courtot.