Ancient DNA reveals Han migration and multi-ethnic admixture in the Hehuang region during Han dynasty

• YJZ genomes show predominant ancestry from Yellow River farming populations. • Northern steppe ancestry in some individuals indicates admixture with pastoralist groups. • Han migration policies substantially shaped local genetic makeup, promoting population admixture. The Hehuang region, at the confluence of the Tibetan and Loess Plateaus, has long served as a frontier linking northern Chinese agricultural communities with steppe and highland groups. To investigate population structure during the Han period, we analyzed genome-wide ancient DNA from nine individuals at the Yangjiazhai (YJZ) site. Most YJZ individuals (YJZ-g1) carry predominant Yellow River-related ancestry, consistent with ancestry from Central Plains agricultural populations, while subgroups (YJZ-g2, YJZ-A977) show affinities to northeastern Asian and Xianbei-related populations, indicating admixture with northern groups. Integration of osteological data and historical records reveals a skewed male-to-female ratio at YJZ, which is consistent with its potential role as a frontier military settlement. These findings provide genetic evidence that Han state-directed migration policies substantially shaped the local population. Overall, YJZ was both a recipient of Yellow River-related ancestry and a genetic contact zone shaped by interactions among agriculturalists, pastoralists and hunter-gatherers, illustrating the demographic impact of Han imperial policies on frontier populations.