The serologic findings in flying-foxes, in conjunction with the molecular findings in insectivorous bats, suggest that ebolavirus infection is taxonomically widespread in Philippine bats. Also, while ebolaviruses have previously been detected in other Pteropodidae, this is the first reported detection in flying-foxes. The stronger serologic response of one sample to EBOV than RESTV antigen in the Western blot is intriguing, and parallels recent findings from Rousettus fruit bats in Asia [10]. While acknowledging the potential for non-specific binding in the recombinant N protein-based Western blot, and for cross-reactivity with heterologous antigens [16], the findings could suggest that more than one strain of ebolavirus is circulating in the source population. All three Western blot corroborated seropositives were A. jubatus, and all were captured at the same roost, which is periodically shared with P. vampyrus. The uncorroborated ELISA-positive bat was a captive P. vampyrus from a different location. This scenario supports the veracity of the serologic findings. Additional samples are needed to further interpret the findings. The absence of positive serology in M. schreibersii given the positive PCR findings warrants discussion. In an endemic infection scenario, positive serology would expected in the source population from which viral RNA was detected. However, in a scenario of recent introduction of infection to a population, limited seroconversion in the presence of infected individuals would not be unexpected. The lack of sequence variation in all three PCR-positive M. schreibersii is consistent with the latter.