Hunting is one of the greatest threats to nonhuman primates worldwide. Despite Madagascar’s status as a primate mega-diversity country, a critical lack of information on the hunting of lemurs at the national scale persists. Here, we synthesize the current state of knowledge of the annual rates of household-level lemur hunting near ten protected areas, representing most ecoregions in Madagascar. We examine geographic and taxonomic variation in lemur hunting, including an analysis of hunting relative to species density, extinction risk, and intrinsic ecological characteristics of species. We found that lemurs are commonly hunted across Madagascar; the rural households in our study ate, on average, more than one lemur each year, or a median of 4.1% of the lemur species’ population size where densities are known. However, this pressure varied significantly across sites and species, reaching its highest levels in the northeastern rainforest region. While hunting levels are concerning for numerous threatened species, hunting pressure was driven primarily by species availability, and among ecological traits, small body size was related to increased hunting; however, conservation status showed no such relationship. This first national-level assessment of hunting, including one-third of Madagascar’s lemur species and more than a tenth of the world’s primates, identifies regional variation and lemur taxa at acute risk from hunting—important steps toward developing targeted strategies to conserve one of the world’s most threatened groups of vertebrates.