In many cases microbes adapt rapidly to new environment and anthropogenic stresses. The understanding of the nature of genetic variants involved in this adaptation and the resulting evolutionary outcomes are both of broad importance for Health and Agriculture. Here we study the ascomycete fungus Zymoseptoria tritici, the causal agent of Septoria Tritici Blotch, a major disease of wheat across the world. Z. tritici is a haploid fungus with a peculiar genome of nearly 40Mb consisting of 13 core chromosomes and up to 8 small AT-rich accessory chromosomes which are dispensable. A thorough study combining phenotyping natural isolates and NGS sequencing revealed loci conveying adaptation to host resistance, thermal and antifungal stresses. In addition we provide empirical evidence that a large inversion on chromosome 7 is quasi fixed in one population, comprising more than a hundred polymorphic sites with strong Fst near 1 and a cytochrome p450 gene involved in antifungal resistance. Here we evidenced a chromosomal inversion that varies along a latitudinal cline and is associated with adaptive trait. To sum up, we add on more empirical evidence that chromosomal inversions can facilitate rapid response by maintaining adaptive alleles and promote local adaptation. These findings highlight the importance of chromosomal rearrangements in response to stress.