It is considered a least-concern species by the IUCN, though its numbers have been negatively impacted by what appeared to be a disease, as well as by hunting for bushmeat that occurs across its range.

[7] In 1889, British zoologist Oldfield Thomas described Pteropus coronatus from a specimen collected on Mioko Island.

However, Andersen noted that it was an immature great flying fox with an unusually pronounced and well-defined T-shaped dark patch of fur on its head, and thus P. coronatus was a synonym of P. neohibernicus.

Pteropus papuanus, described in 1881 by Peters and Italian naturalist Giacomo Doria, was maintained as a separate species by Andersen, though he noted that the only real difference between the two taxa was that P. neohibernicus had paler fur on its back.

[7] American biologist Colin Campbell Sanborn described P. sepikensis in 1931 from a specimen collected near the Sepik River in northeastern New Guinea.

[5] In 1954, British mammalogists Eleanor Mary Ord Laurie and John Edwards Hill published that they considered Pteropus papuanus a subspecies of the great flying fox, Pteropus neohibernicus papuanus, and that P. sepikensis should be tentatively regarded as a subspecies of P.

[8] In 1979, American zoologist Karl Koopman published that he found no differences between P. n. papuanus or P. m. sepikensis and P. n. neohibernicus, and thus, both should be regarded as synonyms of P. n.

The disagreement of nuclear and mitochondrial evidence suggests that the six species may have a complicated evolutionary history.

As the great and spectacled flying foxes both occur in New Guinea, for example, hybridization between the two at points in history would muddle their evolutionary relationships.

[7] It lacks a tail,[3] and has a long, narrow snout relative to the black-bearded flying fox.

The russet brown fur is interspersed with a variable sprinkling of buff-colored (brownish yellow) hairs.

[7] The great flying fox is highly gregarious, or social, and forms colonies consisting of several thousand individuals.

It has been speculated that the sexes may segregate into different roosts in part of the year, similar to the insular flying fox, though this is unconfirmed.

[14] It is known to be parasitized by nematodes of the genus Litomosa, with the species L. hepatica newly described from a great flying fox.

The mass mortality event continued for several weeks across the entirety of the island; afterward, no great flying foxes were seen for several years.

[21] Localized hunting occurs over a large part of its range, with higher levels in East Sepik Province.

[1] A report from 1984 noted that local peoples caught the bats by hand, as well as killed them with arrows.