Patterns of genetic diversity offer insights in the past history of species and their future evolutionary potential. The Italian peninsula is a widely recognised genetic diversity hotspot and one of the main glacial refugia for European temperate trees, which are expected to be severely threatened by climate change. Here, focusing on the wych elm (Ulmus glabra Huds.) in its Italian range, we combined whole plastome-based phylogeography with lineage-based ecological niche models (ENMs), aiming to: 1) identify the main phylogenetic lineages and past glacial refugia along the Italian peninsula; 2) evaluate the future response of the different lineages to changing environmental conditions; 3) develop effective conservation measures for the species, integrating genetic and ecological information. We analysed 75 wych elm trees across the whole Italian range, finding 42 haplotypes clustered in three main haplogroups: 1) ‘Alpine’; 2) ‘North-central Apennines’ and 3) the ‘South-central Apennines’. The high genetic diversity and significant Nst and Gst statistics (0.867 and 0.086, respectively, p≤0.01) revealed a strong phylogeographic pattern with a deep separation between the Alps and Apennines, suggesting a multiple refugia scenario. In the South-central Apennines, the higher nucleotide diversity suggested a ‘refugia-within-refugia’ pattern. Niche overlap and equivalency test highlighted differentiation between Alpine and Apennine wych elm niches (D=0.178). ENMs for the two main lineages predicted a future decrease in habitat suitability mainly for areas in South-central Italy, raising concern for their diverse and peculiar haplotypes. Our findings may inform effective long-term preservation strategies of the wych elm in one of its genetic diversity hotspots.