The origin of Taiwanese aborigines remains obscure; it has been speculated that they may be from either mainland China or southeastern Asia. We used the JCV genotyping method to elucidate the origin of Bunun aborigines who now live in central mountain areas of Taiwan. We found that Bunun aborigines carried two major (B1-a2 and CY) and two minor JCV genotypes (B1-a1 and SC). This was contrasted with the JCV genotype profile in modern Taiwanese: one major (SC) and two minor genotypes (CY and B1-a1). It thus appears that B1-a2 and CY are indigenous to the Bunun tribe. B1-a2 was first identified in this study as a discrete cluster that contained only Bunun and Philippine JCV isolates and that was closely related to B1-a1, one of the three common JCV genotypes in China. CY predominates in North China, while SC predominates in South China and southeastern Asia. The present findings suggest that the Bunun tribe is an admixture of two ethnic groups, one carrying B1-a2 and the other carrying CY. In other words, it is likely that the Bunun tribe was established by two waves of immigrations from mainland Asia, predating those by southern Chinese which began in the 17th century.