[5] The species is considered critically endangered,[6] and if the population trend is maintained, Christmas Island flying foxes are likely to become extinct in the near future.

[2] In 1940, British zoologist Frederick Nutter Chasen demoted all Pteropus in the region to subspecies of the black-eared flying fox, though he expressed some doubts on the validity of P. melanotus natalis.

[2] It is generally covered in deep shining black fur, but the body has a slightly browner tinge than the head.

Generally only one pup is born, and given infant mortality, an individual, on average, has to breed for several years to avert sub-replacement fertility.

This may be due to a lack of predators on the island and an overall low natural mortality rate, which would make it more beneficial to delay development in order to prolong lifespan.

British palaeontologist Charles William Andrews, on his 1897 visit to the island, reported hundreds of flying foxes covering a dead tree.

[15] In 1947, British naturalist Carl Alexander Gibson-Hill also reported the flying fox as plentiful, and described them as somewhat of a nuisance for destroying fruit crops, especially papaya.

[16] The former three of the six colonies (Middle Point, Daniel Roux Cave and Ethel beach) seem to have been abandoned, and the remaining housed no more than 500–1,400 individuals.

It primarily feeds on fruit (frugivory) and nectar (nectarivory), sourced from 35 native plants and 18 introduced, which increase productivity in the wet season from December to March.

Island-dwelling flying foxes, in general, may be the only animals on their island responsible for pollination and seed dispersal for local plants, acting as keystone species.

There is a report of a nonpathogenic coccidia protozoan infection, which is only recorded in 15 other bat species, and an unidentified ascaridid roundworm, possibly the deadly Toxocara pteropidis.

For example, the construction of a casino and possible losses to specific food resources is implicated in the abandonment of the Ethel Beach colony.

[18] Several invasive species have been introduced to Christmas Island, including the barking gecko, Oriental wolf snake, African giant snail, black rat, feral cat, yellow crazy ants, Tanzanian blue ringleg centipede.

However, though feral cats are known to consume the flying fox, there is no evidence they are actively hunting native wildlife;[23] the yellow crazy ant, which sprays noxious formic acid, has formed destructive supercolonies, but while behaviour such as scratching increase in response to the presence of the ant, the flying-foxes do not relocate to different trees or different sites, indicating either minimal disturbance or maladaptive tolerance due to island tameness.

[24] Nonetheless, these invasive species have the potential to negatively impact the ecosystem via habitat alteration, outcompetition, over-predation, or acting as disease vectors.

[20] Ant supercolonies have been aerially bombed with the toxic insecticide Fipronil[16][21][22] (but it has unknown effects on the flying fox)[18] Strong gale-force winds sweeping the island on 27 March 1988 coincided with the estimated start of population decline around 1988, and it was proposed that this destroyed colonies overnight and swept some bats off to sea.

Ingestion of sufficient quantity, possibly through licking off the dust while grooming or consuming dust-covered food, can lead to cadmium poisoning and liver problems.

One roost near a phosphate drier was abandoned, and one Christmas Island flying fox liver was found to contain 0.69 mg/kg cadmium, which is higher than the 0.06–0.48 mg observed in various lab and wild animals, but lower than the toxic threshold, though even trace amounts can be harmful.