Global biodiversity is facing unprecedented threats, partially due to climate change, with tropical and arid-zone species among the most vulnerable. In regions like Saudi Arabia, extreme temperatures and limited water availability amplify these risks, particularly for native desert flora. This study aimed to assess the current and future potential distributions of Ochradenus baccatus Delile and its co-occurring species Vachellia tortilis (Forssk.) Galasso & Banfi. Species occurrence data were compiled from field surveys, GBIF, and literature sources, and ecological niche models (ENMs) were developed using MaxEnt. A suite of bioclimatic, edaphic, topographic, and anthropogenic variables was used, and future projections were generated under SSP2-4.5 and SSP5-8.5 climate scenarios. Variable selection was optimized through correlation analysis and Jackknife testing to ensure robust model performance. The MaxEnt models demonstrated high predictive accuracy, with AUC values exceeding 0.90 for both species. Results indicated that temperature seasonality (bio4), minimum temperature of the coldest month (bio6), and precipitation variables (bio12, bio14) were key predictors influencing the distribution of both species. O. baccatus showed higher dependence on edaphic factors such as soil organic carbon and nitrogen, whereas V. tortilis exhibited broader ecological tolerance. High-suitability zones for both species were concentrated along the western mountainous escarpments, particularly in Al Madinah, Makkah, Al Bahah, and Asir. Future projections for the mid-century (2041-2060) and late-century (2061-2080) periods under SSP2-4.5 and SSP5-8.5 scenarios revealed a substantial decline in suitable habitat area for O. baccatus and increasing fragmentation of co-occurrence zones. The species' high-suitability habitats are projected to shrink and shift toward east-central and northern regions. In contrast, V. tortilis is predicted to retain most of its range along the western escarpment but to experience moderate range contraction and northward redistribution. Consequently, shared high-suitability zones become increasingly isolated, particularly under high-emission scenarios. Hotspot analysis identified climatically stable regions along the southwestern highlands that may serve as future refugia. These areas represent priority zones for conservation planning, habitat restoration, and the establishment of climate-resilient management strategies to preserve Saudi Arabia's desert biodiversity under changing climatic conditions.