This study presents a model investigation into the development of tolerance to polyene antifungal drugs (nystatin and natamycin) in strains of Malassezia pachydermatis. This species, commonly associated with external ear canal infections in dogs, has emerged as increasingly significant in the broader context of growing fungal resistance to treatment. In the experiment, 10 strains of M. pachydermatis were passaged over a period of 105 weeks on media containing sublethal concentrations of nystatin and natamycin. Minimal inhibitory (MIC) and minimal fungicidal concentration (MFC) values were regularly assessed to monitor tolerance development. The results revealed a varied response among the strains: Some were eliminated during the process, while others showed a gradual increase in MIC values, up to fivefold in the case of nystatin. In several strains, acquired resistance remained stable even after passaging in drug-free conditions, whereas others reverted to their original susceptibility. The model demonstrated that resistance does not emerge immediately; significant changes appeared only after 30–45 passages. The authors propose this model as a valuable tool for tracking sequential changes that lead to resistance development. Such an approach may support targeted therapy development and help identify strains predisposed to drug adaptation. These findings hold promise for assessing therapeutic risk in immunosuppressed patients and for building resistance datasets that can support artificial intelligence algorithms in predicting fungal resistance mechanisms.