Conservationists are raising concerns over high lion Panthera leo mortality and prey population declines in the area at the frontier between the Democratic Republic of Congo and Uganda. Confirming if threats to lions are severe or lion populations are disappearing requires extensive surveys on the ground because aerial detection of lions is inaccurate. Yet, ground surveys over large areas are unsafe or infeasible in the war-torn study area. We used aerial surveys of medium- to large-bodied ungulate prey to estimate lion abundance in two adjoining parks: Queen Elizabeth National Park, Uganda, and Parc National des Virunga, Democratic Republic of Congo. We validated two approaches to predict lion abundance using total counts of lions from Uganda. From this, we predict the two national parks together could have held 221 lions in 2004 and they have the potential to hold 905 lions if prey recover and lion-specific mortality is curbed. This makes the region a potential stronghold for the species in central Africa. However, a recent one third decline in lion numbers in the Ugandan Park and pervasive threats to the Congolese Park lead us to recommend immediate conservation intervention for lions and their prey. In Uganda, we recommend focused action to protect lions from poaching and retaliation, whereas in Congo, general enforcement of wildlife protection and a ground-based survey for lions are needed.