
The Amami thrush is a member of the thrush family Turdidae. It is endemic to the islands of Amami Ōshima and Kakeroma island in the northern Nansei Islands of Japan.

The Amami woodcock is a medium-sized wader. It is slightly larger and longer-legged than Eurasian woodcock, and may be conspecific.

The Bonin grosbeak or Bonin Islands grosbeak is an extinct finch. It is one of the diverse bird taxa that are vernacularly called "grosbeaks", but it is not closely related to the grosbeaks sensu stricto. Many authorities place the species in the genus Carpodacus, but some place it in its own genus, Chaunoproctus. A 2013 genetic analysis found it to be a relatively basal member of the group, more derived than the common rosefinch, but with no close relatives, with an estimated divergence time from other members of the group around 12.5 million years ago.

The Bonin nankeen night heron is an extinct subspecies of the nankeen night heron.

The Bonin white-eye or meguro (メグロ) is a small songbird endemic to the Bonin Islands of Japan. It is the only species in the genus Apalopteron. Its taxonomic affinities were a long-standing mystery and it has been placed with the bulbuls, babblers and more recently with the honeyeaters, during which it was known as the Bonin honeyeater. Since 1995 it is known to be a white-eye in the family Zosteropidae, that is closely related to the golden white-eye of the Marianas Islands.

The copper pheasant or Soemmerring's pheasant is endemic to Japan. The scientific name commemorates the German scientist Samuel Thomas von Sömmerring.
The green pheasant, also known as Japanese green pheasant, is an omnivorous bird native to the Japanese archipelago, to which it is endemic. Some taxonomic authorities still consider it a subspecies. It is the national bird of Japan.

The Izu thrush or Izu Islands thrush is a bird of the thrush family native to Japan.

Lidth's jay or the Amami jay, is a passerine bird in the family Corvidae, native to Japan.

The Mukojima white-eye, incorrectly known as the Mukojima honeyeater, is the extinct nominate subspecies of the Bonin white-eye. It occurred on Muko-jima and Nakodo-jima in the northern group of the Ogasawara Islands. The last record were specimens taken in January 1930 on Muko-jima; by then, the bird was already gone from Nakodo-jima. In 1941, the subspecies was found to have gone extinct in the meantime.

The Okinawa rail is a species of bird in the rail family, Rallidae. It is endemic to Okinawa Island in Japan where it is known as the Yanbaru kuina . Its existence was only confirmed in 1978 and it was formally described in 1981 although unidentified rails had been recorded on the island since at least 1973 and local stories of a bird known as the agachi kumira may refer to this species.
The Okinawa woodpecker , is a woodpecker endemic to the Okinawa Prefecture of Japan. It was previously placed in the monotypic genus Sapheopipo.

The Ryukyu robin is a bird endemic to the Ryūkyū Islands, of Japan.

The Ryukyu minivet is a species of bird in the family Campephagidae. It is endemic to Japan. The species was previously thought to be a subspecies of the ashy minivet. Its specific name is named for the Japanese naturalist Seiichi Tegima.

The Bonin thrush, also known as Kittlitz's thrush or the Bonin Islands thrush, is an extinct species of Asian thrush. It is sometimes separated as the only species of the genus Cichlopasser. The only place where this bird was found was Chichi-jima in the Ogasawara Islands; it might conceivably have inhabited Anijima and Otōtojima, but this has not been borne out by observations or specimens. The species was only once observed by a naturalist, its discoverer Heinrich von Kittlitz. He encountered the thrush in the coastal woods where it usually kept to the ground; it may have been ground-nesting. The only specimens ever taken are in the Naturalis in Leiden (1), the Naturhistorisches Museum in Vienna (1), the Senckenbergmuseum in Frankfurt (1) and in the Zoological Museum, St. Petersburg (2).
Japanese green woodpecker or Japanese woodpecker is a medium-sized woodpecker similar and closely related to the European green woodpecker, but endemic to Japan.