Objective To study genetic polymorphism of 6 Y chromosomal STR in Hui ethnic group living in Ningxia Hui ethnic autonomous region, in order to evaluate their usefulness in forensic science and enrich the Chinese genetic information resources. Methods We investigated 101 unrelated, healthy, male individuals of Hui ethnic group and studied their allelic frequency distribution and haplotype diversity of 6 Y chromosomal STR. Primer for each loci was labeled with the fluorescent by FAM (blue) or TAMRA(yellow). The data of Hui ethnic group were generated co-amplification, GeneScan, genotype, and genetic distribution analysis. Results 31 alleles and 43 phenotype(DYS385) were detected, with the frequencies ranging from 0.0099-0.7129. Out of a total of 101 individuals, 96 showed different haplotypes; 91 were unique; 5 were found 2 times. The haplotype diversity for 6 Y-STR loci was 0.9990. Conclusion The date obtained can be valuable for individual identification, paternity testing in forensic fields and for population genetics because of 6 Y-STR loci high polymorphism.