Two new species of flying foxes (genus Pteropus) from the Samoan archipelago are described on the basis of modern museum specimens collected in the mid-19th century. A medium-sized species (P. allenorum, n. sp.) is introduced from the island of Upolu (Independent Samoa), based on a specimen collected in 1856 and deposited in the Academy of Natural Sciences of Philadelphia. It has not been collected again, and we regard it as almost certainly extinct. This species is smaller bodied and has much smaller teeth than both extant congeners recorded in the contemporary fauna of Samoa (Pteropus samoensis and P. tonganus). The closest relative of this new species may be Pteropus fundatus of northern Vanuatu. The disjunct historical distribution of these two small-toothed flying foxes (in Vanuatu and Samoa) suggests that similar species may have been more extensively distributed in the remote Pacific in the recent past. Another species, a very large flying fox with large teeth (P. coxi, n. sp.), is described from two skulls collected in Samoa in 1839–1841 during the U.S. Exploring Expedition; it too has not been collected since. This robust species resembles Pteropus samoensis and Pteropus anetianus of Vanuatu in craniodental conformation but is larger than other Polynesian Pteropus, and in some features it is ecomorphologically convergent on the Pacific monkey-faced bats (the pteropodid genera Pteralopex and Mirimiri). On the basis of eyewitness reports from the early 1980s, it is possible that this species survived until recent decades, or is still extant. These two new Samoan species join Pteropus tokudae of Guam, P. pilosus of Palau, P. subniger of the Mascarenes, and P. brunneus of coastal north-eastern Australia as flying foxes with limited insular distributions that survived at least until the 19th century but are now most likely extinct.