Estimates of population size are necessary for effective management of threatened and endangered species, but accurate estimation is often difficult when species are cryptic. We evaluated effectiveness of mark–recapture techniques using the Lincoln–Peterson estimator for predicting true census size of a population of tuatara (Sphenodon punctatus), a burrowing reptile that is a conservation priority in New Zealand. We found that Lincoln–Peterson estimates (N ˆ  =  85) were accurate for predicting the census size (N  =  87) after only a 3-day mark–recapture survey. We recommend this method as a cost-effective way to accurately estimate population size for isolated, inaccessible tuatara populations, because it requires limited personnel, expertise, and time, and has low environmental impact on fragile sites.