Hunting is a major threat to wildlife, and the use of dogs for subsistence hunting may significantly impact wildlife. I assessed the impacts of hunting with dogs by comparing the assemblages of species hunted by the Huni Kuin with and without dogs in indigenous lands in southwestern Brazilian Amazonia. I also assessed whether Huni Kuin agreements on hunting with dogs can be effective for conservation. Huni Kuin hunters with dogs rely on a different assemblage of prey than those without dogs; the former strategy targets mainly fast-reproducing, resilient species, whereas the latter method kills several sensitive or threatened species. Hunting with dogs is also limited to disturbed mixed landscapes near villages because the dogs are used to protect crops and are not allowed into forests in order to prevent them from becoming lost. Additionally, compared to hunting without dogs, hunting with dogs results in an equivalent amount of meat with the use of less effort and ammunition. Moreover, hunting with dogs is not associated with an increase in the distance of prey from villages. Therefore, there is no conservation-related reason to prohibit hunting with mixed-breed dogs in subsistence communities. Nevertheless, community agreements mediate local conflicts caused by the social inequalities related to hunting with dogs.