Noninvasive genetic sampling is a powerful and effective technique for the study of elusive or otherwise difficult to monitor species. While such methods are widely used in birds and mammals, they have never been successfully applied on a large scale in reptiles. Here we combined scat detection dogs, population genetics, and mark recapture analyses to monitor an isolated and threatened population of the blunt-nosed leopard lizard (BNLL; Gambelia sila) in the Panoche Hills. Once scat samples were genetically confirmed as BNLL, we used multilocus genotyping to identify samples to individual. We used the individual capture data as input for mark/recapture analyses to estimate the population census size. We identified a drastic drop in estimated census size between 2020 and 2021, from 18 (95% CI: 12-23), to 8 (95% CI: 7-13) individuals. This data supports the intervention to capture individuals to establish an assurance colony via captive breeding.