The radiated tortoise (Astrochelys radiata), endemic to the spiny forest of southern Madagascar, had virtually never been studied in the wild until the late 1990s. Recent research projects and surveys have contributed to defining the extent of the decline of the species, and it now appears that A. radiata faces serious extinction risks unless current trends are halted. As part of an ongoing conservation genetics project concerning the species, we investigated genetic diversity and differentiation of the isolated tortoise population from Parc National d'Andohahela (PNA), considered as one of the last remaining sanctuaries of the species in the southeast, where Antanosy people consume tortoise meat. Genetic diversity at PNA was similar to other populations, but differentiation was the greatest of all sites sampled, emphasizing the conservation value of this population. However, our most important finding was that the majority of captured tortoises at PNA were relatively small males, indicating that recruitment may be very low. We found physical evidence that Antanosy poachers are removing the largest individuals from the population, despite their official protection within the park. We discuss conservation issues related to A. radiata, including the role of protected areas in Madagascar, the importance of understanding the taboo toward tortoises in Antandroy and Mahafaly communities, and the pertinence of the current Convention on International Trade in Endangered Species listing of the species.