The golden lancehead pitviper (Bothrops insularis) is a critically endangered species endemic to the Queimada Grande Island, a federally protected area located 33 km off the southern coast of São Paulo State, Brazil. Adults have specialized diet, preying upon migrating birds, and the species' reproductive efficiency is quite lower than its continental related species, B. jararaca. Potential threats to B. insularis include illegal removal, introduction of exotic species or diseases, and catastrophic events such as wildfire. The population size of B. insularis was estimated at 2,899 individuals (CI 95% = 1,903; 4,416) in its forested habitat using distance sampling. This is the first population estimation using 3D area model for a reptile habitat. Bothrops insularis was more sensitive to harvesting of few individuals yearly than a catastrophic event that causes mortality over 95% of the entire population in a 100-year simulation period. Prioritizing conservation efforts of reptile species in Brazil depends on simple yet robust monitoring methods like the one presented here. This study was only made possible through the concatenation of government, management, and scientific interests. Such synergism should be encouraged in conservation policies in Brazil, especially in remote locations.