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Genomic data have increasingly been used to complement linguistic, archeological, and anthropological evidence in reconstructing the origins and migratory patterns of modern humans. East Asia is a particular hotspot of human migration, especially mainland China, where a large number of human fossils have been unearthed and more than 20% of the world’s population now resides. There are 56 officially recognized ethnic populations (minzu) in China. In the present study we investigated the ancestry and genetic diversity of nine populations: the majority Han of Liaoning Province; the Miao, Yao, Kucong, and Tibetan communities of Yunnan Province in southwest China; and four Muslim populations, the Hui, Bonan, Dongxiang, and Sala from central and northern China. We used both biparental and uniparental markers to determine patterns of diversity at autosomal, mitochondrial, and Y-chromosome loci. The study populations displayed several paternal origins but restricted maternal ancestries. From the Y-chromosome data in particular, major demographic changes, such as the Neolithic population expansion and more recent historical events including migration along the Silk Road, could be inferred. Specific aspects of the internal structure and organization of the study populations, including endogamy and consanguinity, were uncovered using autosomal markers. However, we encountered interpretive problems in terms of the definition of the present-day ethnic study populations in China, which appear to reflect past and present political as well as genetic influences.