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Chinese Tajiks are an Indo‐Iranian‐speaking population in Xinjiang, northwest China. Although the complex demographic history has been characterized, the ancestral sources and genetic admixture of Indo‐Iranian‐speaking groups in this region remain poorly understood. We here provide the genome‐wide genotyping data for over 700 000 single‐nucleotide polymorphisms (SNPs) and mtDNA multiplex sequencing data in 64 Chinese male Tajik individuals from two dialect groups, Wakhi and Selekur. We applied principal component analysis (PCA), ADMIXTURE, f‐statistics, treemix, qpWave/qpAdm, Admixture‐induced Linkage Disequilibrium for Evolutionary Relationships (ALDER), and Fst analyses to infer a fine‐scale population genetic structure and admixture history. Our results reveal that Chinese Tajiks showed the closest affinity and similar genetic admixture pattern with ancient Xinjiang populations, especially Xinjiang samples in the historical era. Chinese Tajiks also have gene flow from European and Neolithic Iran farmers‐related populations. We observed a genetic substructure in the two Tajik dialect groups. The Selekur‐speaking group who lived in the county had more gene flow from East Asians than Wakhi‐speaking people who inhabited the village. These results document the population movements contributed to the influx of diverse ancestries in the Xinjiang region. [ABSTRACT FROM AUTHOR]