Abstract To investigate the proposed historical origins of the Hui, a Chinese Muslim minority resident in Liaoning Province, PR China, DNA samples obtained from 53 individuals were analyzed at ten autosomal and six Y-chromosome microsatellite loci. As reference sources, equivalent samples were investigated from the coresident Han majority population. Both the Hui and the Han exhibited appreciable genetic heterogeneity in terms of the size, number, and size range of alleles, suggestive of population substructure resulting from their particular cultural and historical backgrounds. The contrast in the patterns of autosomal and Y-chromosome diversity of the two communities was obvious. Analysis of molecular variance showed that only 4.6% of total autosomal molecular variance was due to differences between the Hui and Han. The comparable value for Y-chromosome haplotype distributions of 14.0% indicated that the Hui and Han of Liaoning have separate paternal genetic histories.