Subalpine ecosystems are centres of endemism that are important for biodiversity. However, these areas are under threat from the creation, expansion and continued modification of ski runs, activities that have largely negative effects on wildlife. Despite this threat, research on the impacts of ski runs is limited for reptiles—particularly regarding the value of remnant vegetation retained on ski runs. Here we quantify the effects of habitat loss and fragmentation (i.e., patch size, patch isolation and edge effects) on the abundance of a common subalpine lizard and on thermal regimes (a key determinant of lizard distribution) in an Australian ski resort. The number of lizards observed differed significantly with habitat type (ski runs vs. forested areas) and patch isolation, but not patch size. In addition, the edges of patches supported more lizards than any other habitat type. These patterns of lizard distribution can be explained, in part, by the differing thermal regimes in each habitat. Ski runs had significantly higher ground surface temperatures than any other habitat type, precluding their use for a considerable proportion of the activity period of a lizard. In comparison, edges were characterised by lower temperatures than ski runs, but higher temperatures than the core of forested areas, potentially providing a favourable environment for thermoregulation. Based on our results, we conclude that although modified ski runs have a negative effect on lizards, patches of remnant vegetation retained on ski runs are of value for reptiles and their conservation could help mitigate the negative effects of habitat loss caused by ski run creation.