Abstract: Background and Objective: Indian desert monitor Varanus griseus koniecznyi Mertens, 1954 is the least common among all the monitor lizards found in India and there is an urgent need to understand habitat attributes and identification of conservation priorities areas of this endangered species. The aim of the present study was habitat suitability analysis of Indian desert monitor in Thar deserts of Rajasthan (TDR). Methodology: Habitat suitability analysis was carried out using GIS-based weighted overlay analysis. Different environmental variables that affect species distribution along with species occurrence data collected from ground survey were used as independent factors in this analysis. Thematic maps for all these factors were used as inputs and finally, all the geo-referenced inputs were overlaid in ArcGIS environment to derive the suitability map. Results: The result showed different potential habitat zones of Indian desert monitor in TDR which are 8.37, 45.55, 38.23, 5.37 and 2.48% as most suitable, moderately high suitable, moderately low suitable, low suitable and unsuitable, respectively. This further revealed, though the species can survive in wider part (most suitable, moderately high suitable, moderately low suitable) of TDR, only a small area of that (8.37%) is best suitable for the species. Of the best suitable habitats, maximum area comes in Jaisalmer district of western Rajasthan followed by Bikaner and Barmer districts. Conclusion: In order to save this conservation dependent species in TDR, the best suitable habitats of the species identified in this study need immediate conservation attention and should be protected from any kind of habitat degradation or alteration in future.