Two species of the Fringe-Toed Lizard, Uma exsul and Uma paraphygas, are restricted to small areas of sand dunes in the Chihuahuan Desert, where land cover transformation has increased dramatically in recent years and future climatic changes are expected to be severe. The current geographic distribution of each species was estimated by ecological niche modeling using the Genetic Algorithm for Rule-set Prediction (GARP). A recent land-use map was used to determine areas where habitat has been transformed by human activities, and niche models were projected under two simulated climatic scenarios and for two periods of time (2020 and 2050) to estimate their future potential distributions. Results indicate a high degree of anthropogenic habitat transformation within the distribution of U. exsul, and an important reduction of its distribution by 2050. For U. paraphygas land cover transformation is less severe, but a complete collapse of its current distributions is expected in the future because of climate change. Despite the uncertainty involved, the general trends seem highly feasible and immediate conservation actions are recommended.