To investigate the genetic structure of 8 Chinese ethnic populations, haplotype data of 9 short tandem repeats (STR) loci on non-recombining region of the Y chromosome (NRY) from 1816 individuals of 12 populations was obtained from the Database of Genome Diversity and Variation for Chinese Populations (HGD-Chn), unpublished data from Key Laboratory of Forensic Sciences and the prior literature. No specific Chinese population groups could be identified through the analysis of molecular variance (AMOVA) based on Y-chromosomal STRs from these samples. Pairwising F(ST) and Nei's genetic distance values were calculated and significant heterogeneity among these populations were observed. The phylogenetic trees were attained based on both the Nei's genetic and pairwising F(ST) values, and pairwising F(ST) based multidimensional scaling plot was also obtained. Several genetic features were observed through the analysis above, and it indicated some further cultural, religious and geographic significance.