The study investigated the adaptation of the snow mold causal fungus, Microdochium nivale, to the fungicides fludioxonil and tebuconazole. Analysis of intrapopulation diversity among 136 M. nivale strains from two Russian populations revealed no strains with high-level resistance to these fungicides. However, the strains exhibited considerable variability in their sensitivity to small fungicide doses. Fungicide sensitivity levels were not associated with virulence levels, whereas strains from different phylogenetic groups exhibited different predispositions to decreased sensitivity to tebuconazole and fludioxonil. In vitro adaptation experiments were conducted to assess: (1) the potential ability of M. nivale to acquire high-level resistance to these fungicides; (2) the relative adaptation efficiency to each fungicide; and (3) the impact of resistance acquisition on virulence. Our results showed that M. nivale strains could adapt to high concentrations of both fungicides with little or no effect on virulence. Adaptation to fludioxonil was significantly less effective than to tebuconazole. To get closer to understanding the mechanisms of fludioxonil adaptation in M. nivale, whole-genome sequencing was performed on a fludioxonil-adapted derivative and its parental fludioxonil-sensitive strain. Comparative genome analysis identified mutations potentially involved in the enhanced fludioxonil resistance, which are discussed within the framework of molecular resistance mechanisms.