<p>Trait variation across environmental gradients provides valuable insights into the ecology and evolution of species. Telomere length is a dynamic trait associated with cellular ageing, stress physiology, and disease risk, among other biological processes. Despite its relevance, it remains poorly characterised in amphibians, particularly concerning intraspecific variation in wild populations. Here, we examined telomere length variation along a montane system of Puerto Rico in the common coqui frog (<i>Eleutherodactylus coqui</i>), a direct-developing species exhibiting variable responses to the infection with the invasive fungus <i>Batrachochytrium dendrobatidis</i>. We quantified telomere length in skin and liver tissues and assessed associations with individual phenotypes and environmental factors. We evaluated alternative hypotheses explaining telomere variation focusing on the skin tissue: tissue-specific cell turnover, phenotypic and infection-related condition, environmental gradients, and an integrated model combining the three of them. Skin telomere length was positively correlated and overall shorter than liver telomere length. Environmental variables, rather than individual condition or infection status, best explained variation in skin telomere length, with frogs at lower elevations and in wetter life zones exhibiting shorter telomeres. Our study provides the first baseline characterisation of intraspecific telomere length variation in coqui frogs. In this context, we revisit hypotheses on how environmental and pathogen-related stressors may shape telomere length, underscoring the evolutionary, ecological, and conservation relevance of these patterns in amphibians.</p>