Y-chromosome short tandem repeats (STRs) are potentially useful for forensic, anthropological and evolutionary studies. In this study we chose the loci DYS 19, DYS 388, DYS 389 I, DYS 389 II, DYS 390, DYS 391, DYS 392, DYS 393, DYS 425 and DYS 426. Blood samples were taken from 46 unrelated male individuals from Fujian Han and 43 unrelated males from Sichuan Han in China. DNA was extracted by conventional chelex extraction procedure. PCR was carried out in two multiplex reactions. Fragment analysis was conducted on an ABI PRISM 310 Genetic Analyzer. Allele frequency distributions and discrimination indices were calculated, and the two populations were tested for genetic differences by means of analysis of molecular variance (AMOVA). Here we obtained 75 Y-STR haplotypes and the haplotype diversity for the complete haplotype was 0.9884 in Fujian Han and 0.9967 in Sichuan Han. A larger genetic difference became apparent between the two populations that belong to the Sino-Tibetan speaking populations.