Anthropogenic disturbances can have negative effects on species assemblages. This study was established to form baseline data on the environmental structure and reptile assemblages within a planned energy corridor in Pinal County, Arizona, prior to construction. We emphasized evaluating the differences in reptile assemblages in two subdivisions of the Sonoran Desertscrub, the Lower Colorado River Valley (LCV) and Arizona Uplands (AZU). Surveys were conducted on 50 sites (LCV = 15; AZU = 35) along the proposed 67.1-km long energy corridor through environmental surveys and 50 drift-fence trapping arrays with 400 box funnel traps. Vegetation height, number of burrows, and percent rock, ground cover, and coarse woody debris were significantly higher in the AZU than in LCV. Eighteen reptile species (n = 995 captures) were detected on the energy corridor including 8 lizard species (n = 952 captures) and 10 snake species (n = 43 captures). Species richness, evenness, and capture rates were not significantly different between the LCV and AZU; however, species diversity was significantly higher in the LCV. Reptile abundance (LCV = 281; AZU = 714) differed in the two subdivisions, yet rank-abundance curves revealed no difference in dominance of species. Post hoc examination revealed that the geographic separation of sites within the LCV and the location of the study area (along the ecotone) may have contributed to our results. We conclude that both subdivisions are equally important to the maintenance of local biotic diversity and recommend that any future land set-asides consider both subdivisions.