Global change is heavily affecting Alpine ecosystems in term of both climate warming and anthropization and its effects have been already demonstrated for many different taxa. However, understanding the genetic consequences on wild species caused by environmental modifications is complicated. In this thesis, I analyzed the genetic variation pattern in two vertebrate species whose distribution and persistence across the Italian Alps could be, or already have been, affected by changing climatic conditions and human pressures for assessing their conservation status. I collected semi-invasive samples of the yellow-bellied toad Bombina variegata and of the common lizard Zootoca vivipara in the central-eastern part of Alpine chain for performing molecular analyses and subsequent statistical inferences. Different types of genetic data were used for different aims, such as mitochondrial and nuclear sequences for confirming the ESU status of a threatened lineage, microsatellite markers for evaluating genetic variability and demographic histories of wild populations or genomic SNPs for studying a major evolutionary phenotypic transition. The analyses suggested that some of the studied populations of both species suffer from reduced genetic variability and low effective population size, even if this pattern is not directly ascribable to recent anthopogenic and climatic changes. In the light of these results, however, specific conservation measure should be evaluated for these species, which are considered of least concern by the IUCN, in particular considering the predicted increase of temperature and expected modifications for their most suitable habitats.