In recent years, several phylogenetic studies on the genus Buteo have been conducted. However, little is known about the lineage of the Eastern Buzzard (Buteo japonicus). We sequenced 919-bp fragments of mtDNA from 45 Eastern Buzzards from Japan and compared them with the sequences of the genus Buteo registered in the DDBJ/EMBL/GenBank databases. ND6 and pseudo control region phylogenetic analyses were performed on 15 and 35 specimens in the database, respectively. All 45 Eastern Buzzards from Japan possessed the same novel sequence in the ND6 gene, which differed in four base pairs from sequences previously reported for the Eastern Buzzard from continental Asia. Phylogenetic analysis of the ND6 gene showed that Japanese birds with the novel sequence did not form a clade with those from continental Asia with the previously reported sequences; instead, the continental Eastern Buzzard formed a clade with Himalayan Buzzards (Buteo refectus). A phylogenetic tree constructed using pseudo control region sequences showed that Eastern Buzzards were divided into two groups: one containing the Himalayan Buzzard, and one containing birds with the novel sequence. Our results suggested that the novel sequence revealed in this study is a geographic variant that may represent the “true” Eastern Buzzard, and that the previously reported sequence (from continental Asia) is that of the Himalayan Buzzard. We suggest that it is necessary to examine the habitats and characteristics of Eastern and Himalayan Buzzards in eastern Eurasia to more accurately classify these birds.