Aim Determining whether altitudinal shifts in species distributions leave molecular footprints on wild populations along their range margins from rear to leading edge. Location South-west France. Methods We compared the demographic and genetic variation in 42 wild populations of the Western oviparous subclade B2 of a cold-adapted lizard (Zootoca vivipara louislantzi). These populations can be divided into four ecological units across altitudinal clines in South-west France (rear edge: <100 m, admixture zone: 100-500 m, continuous range: 500-1,300 m and leading edge: >1,300 m above sea level). Results Within the rear edge were found the highest levels of inbreeding, genetic differentiation and evidence of interrupted gene flow compared to central or colonizing areas. Within the leading edge, altitudinal range expansion occurred over the last centuries and populations showed relatively low genetic diversity. These demographic and genetic trends were better explained by inhospitable (warm and dry) climate conditions and forest cover. Main conclusions This empirical evidence illustrates that molecular footprints of climate conditions and habitat quality on wild population trends can be perceived after recent events, which should be of particular importance to accurately understand and anticipate human-induced global change on wild species and ecosystems.