The Mosuo people are currently the only matrilocal population in China. The origins of the population and their matrilocal tradition remain unknown. To address these questions, we studied the mitochondrial DNA (mtDNA) diversity of the Mosuo. Lower mtDNA diversity is expected in matrilocal populations because the women remain with their families after marriage, and there is generally less movement of mtDNA genomes in matrilocal populations. However, the haplotype diversity of this population is not lower than the neighboring patrilocal populations, indicating that the Mosuo started practicing matrilocality at least after the Paleolithic Age. A previous haplogroup frequency clustering study indicated that the Mosuo are closest to the Naxi people, but the network analysis of individual sequence haplotypes presented herein shows that most Mosuo lineages cluster with Pumi lineages. Therefore, we concluded that the Mosuo people have the closest genetic relationship with the Pumi, and that they started to practice matrilocality several thousand years ago.