There is no documented flying fox hunting study done in the Agusan Marsh Wildlife Sanctuary (AMWS) which is known to harbor many threatened wildlife species. The Large Flying Fox Pteropus vampyrus is known to be threatened by hunting in the AMWS despite existing laws, such as the Wildlife Act. We conducted semi-structured interviews from September 2017 to January 2018 with 240 hunters in 10 villages through purposive sampling to determine the socio-demographic and economic profile of the hunters, their conservation awareness, perceptions on the monitoring scheme and enforcement, possible hunting patterns, and hunting drivers. Results showed that farming and fishing are the most common livelihoods of hunters. Most hunters achieved an education at the elementary level (42.9%), and belong to a household with 4–6 members (55.5%), often with only one member having a meager daily income (80.7%). Annual flooding was the main economic constraint to the hunters. Largely comprised of indigenous Manobos (62.9%), the majority of hunters did not believe in avoiding taboo species (85.4%). Most of the hunters were unaware of laws protecting Wildlife (62.9%) and unable to differentiate between threatened and non-threatened species (86.3%). Poor implementation of the monitoring scheme and insufficient enforcement were also observed in AMWS. Kites with hooks (55%) and guns (31.7%) were used to hunt P. vampyrus mostly for local consumption (83.3%). Multivariate analysis revealed that daily income and engagement in conservation negatively affected hunting intensity. With many constraints in totally banning hunting in poor and wildlife-dependent indigenous communities in AMWS, flexible policies must be considered. It is more reasonable and realistic to consider science-based hunting quotas in policy interventions to balance conservation and human welfare. Positive behavioral change towards sustainable hunting and trading bans requires a combination of effective education campaigns, engagement of indigenous communities in conservation, improved enforcement, and sustainable livelihood programs.