Aim Future climate changes may affect species distribution and their genetic diversity, hampering species adaptation to a new climate or tracking the suitable conditions. Amphibians have high sensitivity to environmental degradation and changes in temperature and humidity. Thus, the expected climatic changes by the end-of-century (EOC 2100) may cause local or complete extinction of some species. Here, we address the effects of climate change on genetic and phylogeographical diversity, together with the geographical distribution of the South American treefrog Scinax squalirostris Lutz, 1925. Furthermore, we assess how protected areas will conserve its genetic variation. Location South America. Methods We combined Ecological Niche Modelling and genetic simulations to predict the effects of climate change on the geographical distribution, genetic diversity, structure and phylogeographical diversity of Scinax squalirostris, using two scenarios of CO2 emission. We also performed a spatial analysis to investigate the effectiveness of the current Protected Areas (PAs) to preserve the species’ genetic and phylogeographical diversity. Results Scinax squalirostris' geographical range will potentially increase in the future due to the expansion of suitable areas towards its southern distribution, despite the shrinking of suitable areas in the northern part of its current distribution. Besides the shifts in suitable areas, our findings point to a genetic homogenization across the geographical range of S. squalirostris due to the displacement and loss of genetic ancestry clusters. Although existing PAs are conserving the current genetic diversity, they conserve less phylogeographical diversity than expected by chance. Scinax squalirostris may shift its distribution into areas with lower number of PAs, compromising its future conservation. Main conclusions Climate change will potentially increase S. squalirostris range size, however, not towards regions where most of the current established PAs are located, hence driving to homogenization and loss of genetic diversity, and leading to a gap of conservation within PAs.