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The genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analyzed in 449 individuals of the Uygur population from Ili Kazakh Autonomous Prefecture, Northwestern China. Phylogenetic analysis was performed among the Ili Uygur population and other relevant populations. The neighbor‐joining tree and multidimensional scaling plot were generated based on the Nei's standard genetic distance. We found a total of 173 alleles with corresponding frequencies ranging from 0.5022 to 0.0011. The combined powers of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999985 and 0.99999880065, respectively. Population comparisons indicated that the Ili Uygur population had a relatively close genetic relationship with the Uygur populations from other regions of China. The pairwise genetic distance and P‐values between Ili Uygur and 10 published populations showed that no statistically significant differences existed between the Ili Uygur population and the Kashi, Kashgar, and Kotan Uygur. Therefore, the Ili Uygur population has its own unique Uygur genetic characteristics that were different from the other ethnic populations of China. [ABSTRACT FROM AUTHOR]