It was formerly considered a subspecies of the grey-capped greenfinch (C. sinica) and some authorities consider it as such, but a 2020 analysis found it likely to represent a distinct species that diverged from C. sinica about 1.06 million years ago, and the International Ornithological Congress now recognizes it as such, making it the eleventh endemic species in Japan (alongside the Copper pheasant (Syrmaticus soemmerringii), Okinawa rail (Hypotaenidia okinawae), Amami woodcock (Scolopax mira), Japanese green woodpecker (Picus awokera), Okinawa woodpecker (Dendrocopos noguchii), Lidth's jay (Garrulus lidthi), Bonin white-eye (Apalopteron familiare), Izu thrush (Turdus celaenops), Ryukyu robin (Larvivora komadori), and Japanese accentor (Prunella rubida)).

[5] The split was implemented in the IOC World Bird List update of January 2021, in recognition of the "deep genetic divergence" and "morphological differences".

[7][14][15] Compared with the Oriental greenfinch, from which the species has been recently split, the wings are shorter and overall body size smaller, but the beak is longer.

[5][14][15] In particular, compared with the Japanese greenfinch (Chloris sinica minor), the beak is "longer, deeper, and thicker".

[14] Among preferred species are Casuarina equisetifolia (as an alien tree, this has recently been eradicated[5]) and in particular Wikstroemia pseudoretusa; since the seeds of the latter are considerably larger than the grass seeds that comprise the majority of the diet of the Japanese greenfinch, it is thought that the larger beak of the Ogasawara greenfinch has evolved in response.

[12] As a restricted-range species, it is particularly vulnerable to extreme weather events such as typhoons and localized droughts, while the small population size threatens genetic diversity.

[14] Invasive brown rats (Rattus norvegicus) and feral cats (Felis catus) are also linked to predation during periods of foraging on the ground, and management of these mammal species has been recommended, alongside ex situ conservation via a captive breeding programme, to reduce the risk of extinction.