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The Oriental Greenfinch Chloris sinica is a passerine bird distributed only in East Asia. Five to eight subspecies are usually recognized: sinica in SE China; kawarahiba in Kamchatka to Kril Is. ; sitchitoensis in Sakhalin; ussuriensis in NE China, Ussuriland to the Korean Peninsula (chaborovi in Amurland is usually lumped with ussuriensis); clarki in Ulleungdo I. in Korea; minor in mainland Japan; kittlitzi in Bonin Is. and Volcano Is. (1,000km south of Tokyo). Our preliminary genetic analysis using DNA barcode region (COI, 650bp) with a few samples showed that population of kittlitzi separated from other populations distinctly. To confirm this with more certainly, we analyzed partial ND6 to cyt b and Control region (CR) sequences of mtDNA through it’s breeding range (n = 86), and other closely related species. As a result of cyt b analysis, all population of C. sinica is formed a monophyletic group against other relatives (C. chloris, C. spinoides and C. ambigua). Within C. sinica, population was split into 2 groups, kittlitzi and the remaining populations (subspecies) with strong bootstrap support. In contrast, relationship among remainder was unclear (same result of CR). To clarify this relationship, further analysis using more higher rate genetic maker (e.g. microsatellite) is needed. The uniqueness of kittlitzi was also supported by it’s morphometrics and plumage, it has short wing length, large beak and different wing color pattern as compared with other subspecies. We conclude that kittlitzi might be treated as distinct species, because it has been separated from other subspecies with considerable long time, probably the Pleistocene, as well as with different external feature. Subspecies kittlitzi has very limited distribution range, distributed only in part of Bonin Is. and Volcano Is. The estimate population size is 200 to 400 individuals, and specified as Critically Endangered in Japanese Redlist. Immediate conservation activities is required for this species.