To gain insight into the social organization of a population associated with the Dawenkou period, ancient DNA analysis of 18 individuals from human remains from Fujia site, Shandong Province, China was completed. Directly radiocarbon dated to 4800–4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y-chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage were de-emphasized compared to the bonds of descent at Fujia