Two hundred and thirty samples from five minority populations resident in Yunnan Province, PR China (the Mosuo, Mongolian, Naxi, Pumi and Tibetan communities) were analysed at eight polymorphic Y chromosome short tandem repeats (Y-STRs) loci. A total of 59 alleles were identified, with the largest number (n = 44) in the matriarchal Mosuo community. Two or three Y alleles were specific to each population. One hundred and thirty-five haplotypes were constructed, with 45 haplotypes in Tibetans, 34 in the Mosuo, 29 in Mongolians, 26 in the Pumi and 17 in the Naxi. The Tibetan and Mosuo peoples were closest in the neighbour-joining tree, whereas the Mongolians differed from the other four populations, reflecting their origins and present-day geographical location in Yunnan.