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Aim To reconstruct the historical biogeography of Hyla molleri, a tree frog endemic to the Eurosiberian and Mediterranean bioclimatic zones in the Iberian Peninsula. Location Iberian Peninsula. Methods We used molecular data (mtDNA and species-specific, polymorphic microsatellite loci) and species distribution modelling (SDM) from the Last Interglacial (LIG) to the present to characterize spatial patterns of genetic diversity in this species and assess their relationship with climatically favourable areas through time. Results Genetic diversity is heterogeneously distributed across the range of H. molleri, with two main genetic reservoirs located in (a) central and southern Portugal and (b) a fragmented area encompassing mountainous areas in northern Spain. According to SDM, the Iberian Peninsula has experienced a progressive and continuous decrease in climatically favourable areas for H. molleri since the LIG, especially in southern and eastern Iberia, where the species is currently absent. However, we found no correlation between areas that have remained climatically favourable since the LIG and current genetic diversity. Main conclusions Our results suggest that the demographic history of H. molleri since the Pleistocene has been characterized by relative stability, contrasting with the large-scale cycles of extinction-recolonization inferred for other more thermophilous, co-distributed amphibian species in Iberia. Accounting for discordant demographic responses to climatic changes across syntopic species provides new insights about the evolutionary history of amphibian communities in southern Europe.