In India, population of the Indian spiny-tailed lizard is extinct in many parts of its past distribution and currently the species is mainly confined to the desert areas of northwestern India. The present study was carried out from January 2014 to May 2017 in the Thar desert of Rajasthan (TDR) to know the population status and habitat suitability of the species and to assess the threats it faces. For this, population was estimated through active burrow counting in selected 15mx15m quadrats. GIS-based weighted overlay analysis was used for habitat suitability analysis for which habitat and microhabitat information was collected through ‘perambulation’ and ‘quadrat sampling-time constrained’ methods. Threats were documented using various methods viz. through vehicular surveys, perambulation, opportunistic searches and by interacting with local people as well as forest staffs. The species was recorded in six districts of the TDR. The overall density of the lizard was found to be 314.6±142.1 active burrows/ha in the study area. The maximum density was observed in Jaisalmer district (362.5±102.3/ha) and the lowest in Jodhpur district (228.0±49.1/ha). Suitability analysis identified different potential habitat zones of the species in the TDR which are 1.71%, 13.49%, 59.51%, 10.65% and 14.64% as most suitable, moderately high suitable, moderately low suitable, low suitable and unsuitable respectively. Majority of most suitable area found to fall in Jaisalmer district of western Rajasthan that need to be protected immediately. The study also revealed the species has been continuously facing various threats in the TDR that leads to local extinctions.