Ebola and Marburg viruses constitute two of the most important human pathogens and pose a significant threat to public health across the globe. Currently, seven distinct species of filovirus have been identified. For six of them serological or virological evidence has been highlighted in bats. Several species of African, Asian, and European bats have now been identified as probable reservoir hosts for filoviruses. Here, we present an overview of current knowledge on the epidemiology and ecology of bat filoviruses, detailing transmission of filoviruses between bats, spillover of these viruses into humans, and the factors leading to infection of bats. We also discuss technical advances to identify and characterize these viruses from potential animal reservoirs. The knowledge of ecological determinants that would promote infection of these animals by filoviruses is an important issue in order to understand and predict disease emergence at local and regional, spatial and temporal scales.