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Bat species in the genus Pteropus (flying foxes) occur throughout most of Southeast Asia, but little is known about their distribution and patterns of local diversity across much of Indonesia. To help address this problem, a field survey of Pteropus species in Central and West Seram, Maluku Province, Indonesia, was conducted in 2012 and 2013. This study resulted in new records of rare Moluccan bats, including new locality records for four near-endemic species: P. chrysoproctus, P. melanopogon, P. ocularis, and P. temminckii. Together with data from additional specimens, these records provide new information about morphological variation in Moluccan Pteropus. High local diversity of large-bodied bats with restricted geographic ranges raises interesting questions about evolution in Pteropus and about ecological niche partitioning in Paleotropical pteropodid communities. More monitoring efforts in Maluku are needed, as the roosts located during the 2012–2013 survey are some of the only known sites where these species may be found, and none of these sites are located in protected areas. Without updated natural history data and taxonomic revision, proper management decisions cannot be made for any of these threatened species despite mounting anthropogenic pressure on their populations.