Threats to primates result from the complex relationship between ecological processes and the direct and the indirect impacts of humans. Yet we know little about the proportional impacts of hunting and changes to habitat on individual primate species. This knowledge is critical to effective conservation. I used primate surveys, habitat analysis, interviews, and one year of direct observation of hunter behavior and catch to compare the relative impacts of altered habitat and snare trapping on two sympatric lemur species: the two largest-bodied and most endangered lemurs on the Masoala peninsula of Madagascar, Varecia rubra (the red ruffed lemur; Critically Endangered) and Eulemur albifrons (the white-fronted brown lemur; Endangered). Results indicate that alteration of habitat and hunting shape local faunal communities in species-specific ways. While alteration of habitat had a greater effect than snare trapping on the populations of V. rubra, snare trapping had a greater effect than habitat on the populations of E. albifrons. Therefore conservation action plans for V. rubra and E. albifrons may benefit from individual tailoring. These findings illustrate the need to consider the different manners in which habitat change and hunting affect sympatric primate species when designing conservation policy.