To study the genetic polymorphism of nine short tandem repeats (STRs) loci (DXS7130, DXS7132, DXS6804, DXS7423, DXS7424, DXS6789, DXS6799, DXS8378, and HPRTB) on X chromosome in Chinese Yugur ethnic group. The allele and genotype frequency of nine X-STR loci among 120 unrelated individuals (55 female, 65 male) from Yugur ethnic group were analyzed using PCR and followed by polyacrylamide gel electrophoresis and silver staining. The numbers of alleles in the nine X-STR loci were 8, 6, 6, 5, 6, 7, 6, 4, and 6, respectively; the numbers of genotypes in the nine loci were 16, 14, 13, 6, 13, 20, 11, 6, and 12, respectively. The genotype frequencies in females were in accordance with Hardy-Weinberg equilibrium (P>0.05). The nine X-STR loci were relatively abundant in polymorphic information for individual identification, paternity testing and population genetics. A total of 15 haplotypes were detected in DXS7130 and DXS8378 loci, and 55 haplotypes were detected in DXS6789, DXS6799, DXS7424, and DXS6804 loci. The haplotype diversity reached 0.8212 and 0.9947, respectively. Phylogeny tree and cluster analysis based on X-STR allele frequencies in genesis showed that Yugur ethnic group share a close relationship with Mongolian ethnic group and Chinese Han, Tibetan population and far from Hui and Uygur ethnic group, who dwell in the northwest of China.