Aim: Macroscale biodiversity inferences are critical for spatial conservation planning, yet they are affected by the limitations of global datasets and the paucity of genetic data. In this study, we conducted a comprehensive sampling campaign and explored how biodiversity shortfalls impact spatial diversity metrics across a mid-altitude desert ecotone, where mega conservation and restoration projects are underway. Location: AlUla region (NW Arabian Peninsula). Taxa: Terrestrial reptiles. Methods We generated a DNA barcode library including 580 field-collected samples to investigate species distributions, candidate species and intraspecific diversity. Species distributions were mapped using climatic envelopes, while candidate species and intraspecific diversity were assessed with phylogenetic methods. Patterns of alpha and beta diversity were mapped based on IUCN and GARD expert maps (expected diversity) and on an integrative assessment combining field and bibliographic occurrences (observed diversity). Topographic drivers of nucleotide diversity were tested using Generalised Linear Mixed Models. Results: Over one-third of the verified species in the region (n = 58) experienced Linnean, Wallacean or Darwinian shortfalls, including 6 candidate species, 11 new to the region and 7 harbouring significant intraspecific diversity. Additionally, 13 species predicted by expert maps were absent. Both IUCN and GARD projections showed significant mismatches with observed alpha and beta diversity, though GARD provided alpha-diversity estimates closer to observed patterns. Nucleotide diversity increased with absolute altitude. Main Conclusions: Field and genetic-based data significantly enhance biodiversity knowledge and conservation tools for this rapidly developing desert region. By addressing the critical limitations of macroscale approaches in undersampled yet diverse landscapes, we demonstrate how global databases often overlook local community turnovers, misleading diversity estimates. Thereby, we highlight the need for fine-scale integrative research to inform conservation strategies and the power of DNA barcoding for inter- and intraspecific biodiversity assessments.