Widespread hunting of flying foxes has generated concern regarding population declines and the spread of emerging infectious diseases. To investigate the potential impacts of this trade, we conducted ques- tionnaires in 45 settlements across 12 population centres within Central Kalimantan, Indonesia, a region previously identified as a hunting hotspot. By combining results from 63 hunter and 88 vendor inter- views, we highlight two population centres (Palangka Raya and Buntok/Tamiang Layang) with higher hunting rates than other areas, which act as flying fox trading hubs. Flying fox populations were per- ceived to be declining province-wide: declines in captures and sales were reported by 81% of hunters and 60% of market vendors, who also reported availability as the key factor underlying temporal varia- tions in trade. There was substantial risk of zoonotic disease transmission between bats, hunters and traders: the vast majority of respondents were unaware that flying foxes carry potentially fatal viruses, and so few people protected themselves from physical contact. Moreover, both hunters and vendors were frequently bitten and the majority of bites drew blood. Most hunters (58%) also reported unintentional by-catches that included keystone bird species and slow lorises. The scale of hunting over Central Kalimantan represents a serious threat to the long-term viability of flying fox populations (and poten- tially those of other species), and could have serious public health implications. Reducing or eliminating hunting and trade would mitigate the risk of disease transmission, while maintaining the economic and ecosystem benefits that flying foxes provide, in terms of pollination and seed dispersal.