The plant fungal pathogen, Zymoseptoria tritici, has a great ability to adapt to their environment. This is largely explained by the high degree of plasticity of their genome due to the presence of chromosomal rearrangements. We have found that genes encoding CAZymes, effectors and secreted proteins are located in DNA regions associated with a high degree of intergenic distance variation. This mechanism would change the gene expression pattern of these genes and therefore participate in phenotypic changes of Z. tritici strains. Besides, we tested the correlation between the intergenic distance variation and the variation in the level of gene expression of the nearby gene, and we have seen that the presence of indels can lead either an increase or a decrease in the level of gene expression. So, chromosomal rearrangements seem to be involved in the phenotypic changes of the strains by changing gene expression leading to their adaptive ability.