Marburg virus (MARV) and Ravn virus (RAVV), collectively called marburgviruses, cause a rapidly progressive, often fatal hemorrhagic fever in humans. Marburgviruses were first isolated from Rousettus aegyptiacus bats inhabiting Kitaka mine near Ibanda, Uganda, following a Marburg hemorrhagic fever (MHF) outbreak there in 2007. Following this outbreak, the colony was exterminated by local miners in an attempt to regain access to the mine after it was closed due to the presence of the virus. In 2012, MHF reappeared in Ibanda town in the largest outbreak in Uganda to date, resulting in 15 laboratory-confirmed MHF cases. An ecological investigation revealed Kitaka mine had been re-opened and subsequently repopulated by R. aegyptiacus bats. Analysis of bat tissue samples by quantitative reverse transcriptase PCR (qRT-PCR) revealed elevated levels of MARV infections in bats inhabiting the mine after repopulation had occurred. Our findings elucidate that the destruction of a colony of R. aegyptiacus is not an effective control strategy. Permanent non-lethal exclusion practices may prove more effective.