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Habitat heterogeneity is necessary to support reptile species diversity and abundance. In the North American Desert Southwest, there is little information regarding habitat preferences that influence reptile community occupancy. In south central New Mexico, we sampled reptiles on Holloman Air Force Base (HAFB) in relatively undisturbed habitat within gypsum sand dunes and clay/loamy soil to determine species richness and relative abundance using Occupancy Modeling. Species were intensively surveyed using pitfall traps, funnels traps, road cruising and active searching. We found six species of lizards, five species of snakes, and one turtle; lizards being more abundant, particularly the Common Side-blotched (Uta stansburiana) and Little Striped Whiptail (Aspidoscelis inornata) lizards. We also related reptile species assemblages to habitat gradients (cover and soil type) using Canonical Correspondence Analysis (CCA). Uta stansburiana, A. inornata, and Eastern Collared Lizards (Crotaphytus collaris) were the only reptiles observed at a high enough frequency to analyze their habitat associations using CCA. Uta stansburiana had a close association with bare ground, A. inornata was associated with clay/loamy soil, and C. collaris was most closely associated with greater densities of grasses and forbs. There may be confounding influences on the lack of reptile species detected, most notably precipitation, given persistent drought conditions in the Desert Southwest. After rain events resume, it may be necessary to re-examine reptile composition and their habitat associations to investigate the re-establishment and recruitment abilities of these arid-adapted species.