The Madagascar flat-tailed tortoise Pyxis planicauda is threatened with extinction through loss of its deciduous, dry forest habitat and illegal collection for the pet trade. Little is known of the population status of this species as no systematic survey across its range has previously been conducted. Surveying P. planicauda is problematic as it has cryptic colouration, is only active during the wet season, and spends periods of time hidden under leaf litter. In this study we designed a line transect survey, which incorporated an approximation of the amount of time tortoises were available for sampling, to produce an unbiased estimate of population size. We estimated density of P. planicauda in the main forest block in central Menabe, which represents the majority of its range, to be 0.40 ha-1 with a total population size of nearly 28,000 individuals (95% confidence interval 16,323-47,669). This estimate is substantially higher than previous predictions of <10,000 individuals. Nevertheless, the species faces ongoing threats from deforestation and probably from illegal collection, although the recent designation of the Menabe forest as a protected area will probably help reduce these threats. This study provides a baseline density estimate of P. planicauda and a survey protocol for monitoring future population trends.