A major threat to the survival of many reptile species is the consequence of rapid growth of the human population. The acceleration of associated anthropogenic activities causes fragmented and transformed habitats, placing the survival of biodiversity in transformed areas at risk. The sungazer (Smaug giganteus) is a threatened (Vulnerable) grassland specialist lizard species. Its geographic distribution is significantly impacted by agriculture and mining activities, resulting in major threats to the species. We assessed sungazer population demographics and dynamics at four sites, each with different habitat conditions by resurveying sungazer subpopulations first surveyed in 2004. Individuals were marked with passive integrated transponders. Abundance declined by more than 50% at two sites associated with mines and an overgrazed site over the 12 to 16-year period between surveys, and the proportion of recaptures were also the lowest in these sites (<15%). Most recaptured lizards were not found in their original burrows, and most lizards in transformed habitats were found more than 100 m away from their original burrows. Our results highlight the potentially detrimental effects of habitat transformation on sungazer demographics that have not previously been detected. Previous assessments focused on the local extinction of aggregations but not declines in abundance in aggregations that had not yet gone extinct. Our results suggest that the species may be more susceptible to habitat transformation than previously estimated. We recommend careful, continuous monitoring of sungazer subpopulations at fine spatial resolutions such that swift conservation action can be taken.