Objective Through paternal inheritance, to explore the molecular genetic relationships of 11 Y chromosomal short tandem repeat gene loci in 24 populations. Methods 11 Y-STR loci in all samples were amplified with PowerPlex(R)Y System, and the PCR products were analyzed using 310 Genetic Analyzer.Cluster analysis and phylogenetic trees constructed by Neighbor-Joining method were applied to show the genetic distance among the populations. Results Analysis of the haplotype frequencies and studies of genetic distance indicated that 11 Y-STR loci polymorphisms varied notably between Han subpopulations and minorities populations. The phylogenetic tree was similar to the results of clustering analysis and all of the 24 populations were clustered into 3 major groups,plus some minority groups. All of 12 Han populations were clustered into southern Han and northern Han groups. Yunnan Han and Sichuan Han relatively close to northeast Han(0.002 3,0. 000 6), and not to the typical southern Han populations even though they live on theSouth. Hui ethnic alone was another group and other minorities are relatively separated. The result also showed that the populations in Chinese Korean ethnic, Republic of korea, Japan were close to each other(0. 013 3,0. 041 3). Conclusion The 24 different populations have gene communications, and some minorities far scattered as their geographical location;The study of haplotype distance among different populations is useful in research of their origins, migrations and their relationships.