In the present study, we calculated the allelic frequencies and forensic descriptive parameters of Hui ethnic minority on the basis of 21 short tandem repeat (STR) loci aiming at understanding population structure better and enriching population genetic database. Bloodstain samples of 506 unrelated healthy Hui individuals in Xinjiang Uygur Autonomous Region were collected. Altogether 268 alleles were observed and the allelic frequencies ranged from 0.0010 to 0.5306. The combined power of discrimination and the cumulative probability of exclusion of the 21 STR loci in Hui ethnic minority were 0.9999999999999999999999998697 and 0.9999999968, respectively. Population data obtained manifested that the panel of 21 STR loci could provide robust genetic information for individual identification and paternity testing involved in forensic applications for Huis of Xinjiang Region. Furthermore, the present results of interpopulation differentiations, phylogenetic trees and principal component analysis which were conducted based on the overlapping 16 STR loci revealed that Hui group was genetically close to Xibe ethnic group and Han populations from different regions.