The consequences of global climate change can already be seen in many physical and biological systems and these effects could change the distribution of suitable areas for a wide variety of organisms to the middle of this century. We analyzed the current habitat use and we projected the suitable area of present conditions into the geographical space of future scenarios (2050), to assess and quantify whether future climate change would affect the distribution and size of suitable environments in two Pristidactylus lizard species. Comparing the habitat use and future forecasts of the two studied species, P. achalensis showed a more restricted use of available resource units (RUs) and a moderate reduction of the potential future area. On the contrary, P. nigroiugulus uses more available RUs and has a considerable area decrease for both future scenarios. These results suggest that both species have a moderately different trend towards reducing available area of suitable habitats, the persistent localities for both 2050 CO2 concentration models, and in the available RUs used. We discussed the relation between size and use of the current habitat, changes in future projections along with the protected areas from present-future and the usefulness of these results in conservation plans. This work illustrates how ectothermic organisms might have to face major changes in their availability suitable areas as a consequence of the effect of future climate change.