Climate change and human influence are transforming mountain ecosystems, significantly impacting species distributions and biodiversity. Among these changes, the upward migration of lowland species into mountain regions stands out. This study examines the ecogeographical niche overlap and genetic diversity among three Leucanthemum species in the Carpathian Mountains distributed along an altitudinal gradient: the lowland L. ircutianum (4x), the montane L. rotundifolium (2x), and the alpine L. gaudinii (2x). By genotyping over 600 individuals using SNP analysis, followed by Principal Coordinate Analysis (PCoA), Neighbor-Net Network, and Structure clustering, we reveal not just distinct genetic groups but also hybridization across all species, suggesting the potential for triple hybrids. Genetic admixture is further supported by environmental background and niche overlap analyses that reveal substantial overlap among species, particularly in line with their vertical distribution. Climate envelope plots indicate a likely reduction in available habitat for mountainous species due to climate change, leading to an increase in competition and an intensification of hybridization. Anthropogenic influences are further intensifying these hybridization trends. Among the studied species, L. gaudinii is most at risk of overwhelming hybridization, whereas L. ircutianum may experience habitat expansion. By providing a comprehensive genetic and ecological overview, our research highlights the significance of hybridization in biodiversity conservation and the challenges posed by environmental changes and anthropogenic activities in mountain environments. This study not only contributes to the understanding of genetic diversity in the Carpathians but also underscores the broader implications for molecular ecology and conservation strategies in mountain ecosystems.