We present a >50,000-year-old archaeological sequence of hunting from Molol Cave on the island of Waigeo, West Papua, Indonesia. The paper draws from metric comparisons and species identifications, tooth wear analyses and mortality profiles, and taphonomic investigations of cut marks, burning, and breakage patterns to argue that locally abundant megabats (Pteropodidae) were the focus of hunting in each occupation phase, from the Late Pleistocene to the Late Holocene. Alongside these mammals, people hunted a wide array of rainforest fauna during the terminal Pleistocene to mid-Holocene, and collected marine resources in the Late Holocene. The results are discussed in the context of niche diversification and the specialisation in small game hunting in the rainforested islands of Wallacea, Island Southeast Asia, New Guinea, and the Pacific.