Background: Chuanqing is an unrecognised ethnic group in Guizhou, southwest China. The genetic history of the Chuanqing people is hotly debated due to a lack of available genetic data.

Aim: To infer the genetic structure and population history of Chuanqing people and genetic relationships of the Chuanqing with other East Asians.

Subjects and methods: We collected samples from 14 Chuanqing individuals from Guizhou and genotyped about 690,000 genome-wide single nucleotide polymorphisms (SNPs). We used Principal Component Analysis (PCA), ADMIXTURE analysis, and f statistics to infer the population genetic structure and admixture.

Results: Chuanqing people show a distinct genetic profile from indigenous Tai-Kadai and Tibeto-Burman speaking populations in southwest China, but they are genetically similar to southern Han Chinese, Miao, She and Tujia populations. The Han Chinese characteristic Y chromosomal lineages reach high frequencies in Chuanqing.

Conclusions: The genetic formation of Chuanqing people has been greatly influenced by Han Chinese related populations.