Alpine habitats are exposed to increasing anthropogenic pressure and climate change. The negative impacts can lead to chronic stress that can affect the survival and reproductive success of individuals and even lead to population extinction. In this study, we analyse different morphological and ecological traits and indices of abiotic and biotic stressors (such as head size and shape, fluctuating asymmetry, body condition index, tail autotomy, and population abundance) in alpine and subalpine populations of two lacertid species (Zootoca vivipara and Lacerta agilis) from Serbia and North Macedonia. These lizards live under different conditions: allotopy/syntopy, different anthropogenic pressure, and different levels of habitat protection. We found differences between syntopic and allotopic populations in pileus size, body condition index (in both species), pileus shape, fluctuating asymmetry (in L. agilis), and abundance (in Z. vivipara). Differences between populations under anthropogenic pressure and populations without it were observed in pileus shape, body condition index (in both species), pileus size, fluctuating asymmetry, tail autotomy and abundance (in L. agilis). On the basis of our results, it is necessary to include other stress indicators in addition to fluctuating asymmetry to quickly observe and quantify the negative effects of threat factors and apply protective measures.