A genetic study by Yinqiu Cui et al. from 2013 analyzed the Y-chromosome DNA haplogroup based N subclade; it found that DNA samples from 63% of the combined samples from various Hongshan archaeological sites belonged to the subclade N1 (xN1a, N1c) of the paternal haplogroup N-M231 and calculated N to have been the predominant haplogroup in the region in the Neolithic period at 89%, with its share gradually declining over time.Today, this haplogroup is found in northern Han, Mongols, Manchu, Oroqen, Xibe and Hezhe at low frequencies. Other paternal haplogroups identified in the study were C and O3a (O3a3), both of which predominate among the present-day inhabitants of the region.

Nelson et al. 2020 attempts to link the Hongshan culture to a "Transeurasian" (Altaic) linguistic context.According to a study on genetic distance measurements from a large scale genetic study from 2021 titled 'Genomic insights into the formation of human populations in East Asia', hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers, but they did not carry West Liao River farmer ancestry, contradicting the Transeurasian hypothesis proposed by Martine Robbeets et al. that the expansion of West Liao River farmers spread these proto-languages.

A 2020 study discovered substantial genetic changes in the West Liao River region over time. An increase in the reliance on millet farming between the Middle-to-Late Neolithic is associated with higher genetic affinity to the Yellow River basin (generally associated with speakers of the Sino-Tibetan languages), while a partial switch to pastoralism in the Bronze Age Upper Xiajiadian culture is associated with a decrease in this genetic affinity. After the Late Neolithic, there was a sharp transition from Yellow River to Amur River-related genetic profiles (associated with speakers of Tungusic languages) around the West Liao River. This increase in Amur River affinity corresponds with the transition to a pastoral economy during the Bronze Age.

A 2021 study found that Yellow River millet farmers from the modern-day provinces of Henan and Shandong had played an important role in the formation of Hongshan people or their descendants via both inland and coastal northward migration routes.

A 2025 study found that the Hongshan populations inherited genetic contributions from three main sources: Ancient Northeast Asians (ANA), Neolithic Yellow River farmers (NYR), and Shandong hunter-gatherers (Shandong_HG). The ANA-related ancestry likely came from the earlier local Zhaobaogou culture, while the NYR-related ancestry was associated with the Yangshao culture and may have been introduced indirectly by Middle Neolithic farmers from the Dawenkou culture migrating northward from Shandong. These Dawenkou-related farmers carried about 40% ancestry from an early Neolithic Shandong hunter-gatherer lineage and about 60% from a Yangshao-related lineage.