Tujia people call themselves "Bizika", which means aboriginal. Genetic study of Tujia is virtually absent. To characterize the genetic structure of Tujia,the distribution of 14 Y haplogroups was studied in Tujia populations sampled from Enshi, Hubei (31 males) and Jishou, Hunan (68 males). A total of eight haplogroups were observed in the Enshi and Jishou populations. The haplogroup frequencies of Tujia were compared with the frequencies of other related ethnic groups, including Northern Han, Southern Han, Tibetan-Burman speaking populations,Daic and Hmong-Mien. The principal component (PC) analysis was conducted and the PCs were plotted to explore the historical migrations. In addition, partial correlation analysis was performed to study the relationship between the first three PCs and the haplogroups. The PC2 revealed a cluster of Tujia groups including Longshan,Yongshun, and Enshi with Lahu, suggesting possible interaction between Tujia and the Di-Qiang groups. However,a similarity between Han and Tujia populations, though differentiated, were also observed. We postulated, by incorporating the results of archaeological and historical evidences, that the Ba people, the ancestors of the Tujia,might be related with Di-Qiang groups and inhabited the Tujia area initially before a substantial interaction with Han and other ethnic groups.