Roe deer (Capreolus capreolus) are widespread across Europe and exhibit adaptability to various habitats. In the last couple of decades, population numbers have significantly increased, except for certain areas which have experienced population declines due multifactorial reasons, including the impact of fascioloidosis. In Croatia, roe deer are primarily found in lowland region, while their population in mountain areas is smaller and more scattered due to habitat limitations and presence of large predators. The variability of major histocompatibility complex (MHC) genes offers insight into the population's ability to combat new pathogens and to cope with changing environments. Here, we examined the variability and selection patterns of MHC class II DRB locus in roe deer from two distinct habitats in Croatia. Ten alleles were identified in 133 individuals accompanied by high amino acid evolutionary distance (41.1%). The lack of significant structuring on the DRB was observed between the two habitats, with ambiguous results from contemporary and historical selection analysis. Furthermore, our results highlight the need to investigate other immune loci, which could provide insight into the relationship between pathogen-mediated selection and adaptation potential in roe deer.