Natural habitats are rapidly changing due to climate change and globalization. This can break down mating barriers between species and lead to increased hybridization rates. How detrimental or beneficial hybridization is for population fitness and adaptation is usually unknown and depends on genetic and environmental factors. Here, we use a combination of experimental evolution with the model system yeast Saccharomyces cerevisiae and population genomics of natural populations of the filamentous fungi to study adaptation and hybridization. Experimental yeast populations are used to study the dynamics of allele frequencies under stressful environments, using both PoolSeq and whole genome sequencing data. On the other hand, using new sequencing data of Podospora anserina populations and related species, we will study historical demography and hybridization, in particular focusing on a specific class of genes that potentially function as a fungal immune system. Overall, these analyses will contribute to our understanding of adaptation and hybridization both in experimental and natural populations.