The House of Aisin Gioro is the imperial family of the last dynasty in Chinese history-Qing dynasty (1644-1911). The Aisin Gioro family originated from Jurchen tribes and founded the Manchu people before they conquered China. By investigating the Y chromosomal short tandem repeats (STRs) of seven modern male individuals who claim to belong to the Aisin Gioro family (three of which have full records of pedigree), we found that three of them (two of which having full pedigree, whose most recent common ancestor is Nurgaci) showed very close relationship (1-2 steps of differences in 17 STRs) and possessed a rare haplotype. We therefore conclude that this haplotype is the Y chromosome of the House of Aisin Gioro. Further tests of single-nucleotide polymorphisms indicate that they belong to haplogroup C3b2b1*-M401(xF5483), although their Y-STR results indicate that they are not a part of the 'star cluster' (once linked to Genghis Khan), which belongs to the same haplogroup. This study forms the base for the pedigree research of the imperial family of Qing dynasty by means of genetics.