In the Great Basin, invasion by cheatgrass has altered landscape structure and ecosystem function. By usurping resources and modifying habitat, cheatgrass has caused dramatic reductions in plant and wildlife abundance and diversity. Though this pattern of biodiversity loss is clear, the mechanisms and landscape scale implications remain unknown. There is little information on whether cheatgrass impacts reptile communities. We hypothesize that loss of shrub cover in cheatgrass dominated areas will leave fewer thermal microhabitats and temperature gradients for reptiles to thermoregulate. To test this, we developed operative temperature models based on Sceloporus occidentalis to deploy at paired sites (cheatgrass vs. native shrub habitat) in northwestern Nevada.  Cheatgrass dominated sites are, on average, significantly hotter than shrub sites. Reptiles in the Great Basin rely on shrub cover to avoid critically hot temperatures, the loss of such refuges may result in temperatures restrictive for normal activity. Cheatgrass habitat may be thermally unsuitable and represent habitat loss for reptiles. We have identified a plausible mechanism of biodiversity loss due to cheatgrass invasion: modified temperature regimes and loss of thermal microhabitats. Given that 10% of the Great Basin has converted to cheatgrass monocultures, we expect significant regional declines in reptile abundance, diversity and connectivity.