Our new research shows that in rural settings of Madagascar where forested landscapes were converted to agriculture and settlements, the potential transmission of a deadly virus, Hantavirus, is likely facilitated by invasive rodents, especially the black rat. Our results show that black rats were the only species in our system that were infected with Hantavirus, with 10% of sampled individuals infected. Preserving natural forest and facilitating the regeneration of transformed forests may decrease disease risk because infected individuals were rarely captured in natural forests.