Eukaryotic genomes are often described as stable structures with well-preserved chromosome organisation. Consequently, genome instability is viewed as a deleterious event. However, it is becoming increasingly clear that genomes can be plastic, and that genome instability can be advantageous for adaptation to challenging environment. The overall goal of this project was to understand whether and how genome plasticity contributes to environment adaptation in Scheffersomyces stipitis, one of the most promising yeast for the production of second-generation bioethanol. S. stipitis belongs to the CTG clade, formed several yeasts (such as C. albicans) whose genomes have been widely described as plastic. To do so, the karyotype of 27 strains isolated from different habitats and countries was studied by CHEF electrophoresis. This allowed us to discover that two of the most used strains in S. stipitis research (NRRL Y-11545 and NRRL Y-7124) exhibited differences in their genome structures. Therefore, we compared the publicly available genome of the strain Y-11545 to the genome sequence of the natural isolate Y-7124, sequenced in this study by a hybrid TGS approach, based on the combination of Illumina and Oxford Nanopore Technologies (ONT). Moreover, to elucidate whether genomic plasticity conditions short-term evolution in S. stipitis, we analysed the karyotype of strains derived from the natural isolate Y-7124 after an adaptation experiment. Our results prove that the genome of S. stipitis is plastic, since different genome conformations are observed among the natural isolates studied. We have also shown that this plasticity is strongly associated to repetitive regions, at least in the two natural isolates whose genome is available. The major contributors to repetitive regions in S. stipitis genome are transposable elements, altogether with subtelomeres, telomeres, (all of them described in this study for the first time) and centromeres. Moreover we have detected several chromosome modifications: (i) A reciprocal chromosome translocation between the natural isolates Y-11545 and Y-7124 (ii) An aneuploidy consisting of an extra chromosome in the evolved strain Y-50859, (iii) A reciprocal chromosome translocation between the strain Y-7124 and its derived strain Y-50859. Both modifications (i) and (ii) are associated to repetitive DNA. In conclusion this project has demonstrated that the genome of S. stipitis is highly variable, and this plasticity is conditioned by repetitive DNA. Moreover, we have shown that strains with improved phenotypic traits related to fermentation are influenced by genome conformational changes.