In the course of the peopling of the World by Homo sapiens, East Asia was reached about 50,000 years ago (50 kya). The "recent African origin" lineage of 70 kya diverged into identifiable East Eurasian and West Eurasian lineages by about 50 kya. This early East Asian lineage diverged further during the Last Glacial Maximum, contributing outgoing from Mainland Southeast Asia significantly to the peopling of the Americas via Beringia about 25 kya. After the last ice age China became cut off from neighboring island groups. The previous phenotypes of early East Asians became either replaced or prevailed among more geographically distant groups.
 A review paper by Melinda A. Yang (in 2022) summarized and concluded that a distinctive "Basal-East Asian population" referred to as 'East- and Southeast Asian lineage' (ESEA); which is ancestral to modern East Asians, Southeast Asians, Polynesians, and Siberians, originated in Mainland Southeast Asia at ~50,000BC, and expanded through multiple migration waves southwards and northwards respectively. This ESEA lineage gave rise to various sublineages, and is also ancestral to the Hoabinhian hunter-gatherers of Southeast Asia and the ~40,000 year old Tianyuan lineage found in Northern China, but already differentiated and distinct from European-related and Australasian-related lineages, found in other regions of prehistoric Eurasia. The ESEA lineage descend from an earlier "eastern non-African" (ENA) or "Ancient East Eurasian" meta-population, which also gave rise to the Ancient Ancestral South Indians (AASI) as well as to Australasians.
 Han Chinese have Indo-European ancestry in Shaanxi. The study showed Han Chinese have Haplogroup U in Shaanxi. Other Indo-European mtdnas that Han Chinese have W6 and Han Chinese have Haplogroup H in Shaanxi. Han Chinese have R1a1 in Shaanxi as well.  
 The study showed Han Chinese have U mtDNA Haplogroup U in Xi'an city. Han Chinese have R1a1 in Xi'an city. Han Chinese have Haplogroup H in Xi'an city.
 Wang et al. (2021) found that the ancestries of individuals in Guangxi from between 9,000–6,000 BP can be modeled as mixtures of Upper Paleolithic source populations from both Guangxi and Fujian. During the early and late Neolithic, migration of Austronesians from the Fujian region's Neolithic Austronesians significantly influenced the genetic profile of the Guangxi region but did not completely replace the earlier resident hunter-gatherer ancestry that was local to Guangxi. Neolithic Fujian is genetically unrelated to Modern Fujian. The main archaic individuals that were analyzed include the following.
 Huang et al. (2022) associate Dushan and Baojianshan-related ancestry with the first Neolithic farmers in Mainland Southeast Asia (MSEA), i.e. late Neolithic farmers who expanded from southern China into MSEA. Among present-day populations, they found that:
 Guangxi region individuals from 1,500–500 BP show genetic profiles that can be identified with present-day Kra-Dai and Hmong-Mien-speaking populations of southern China. They can be modeled as a mixture of 58.2%–90.6% Dushan-related (or Qihe-3-related) ancestry and 9.4%–41.8% northern East Asian-related ancestry, with the later attributed to relatively recent historical migrations from the north.
 Looking at Y-DNA studies, it would seem that East Asian paternal lineages expanded in Asia approximately 50,000 years ago. People bearing genetic markers ancestral such as C, D, N, and O, as well as P (specifically Q), came through the Himalayan mountain range and proceeded to Southeast Asia. Haplogroup C moved to East Asia and Australia, with at least two subclades of the major East Asian branch migrating into the Americas, and with members of Haplogroup C-M38 spreading throughout Wallacea, New Guinea, Melanesia, and Polynesia. Another group of peoples, bearing the Y-DNA Haplogroup D, has left descendants mostly in the Andaman Islands, Tibet, and Japan. Haplogroup Q, believed to have arisen in Central Asia or Southern Siberia approximately 17,000 to 22,000 years ago, went north to populate Northern Siberia and the Americas. Some northern Chinese have this genetic marker. Haplogroups N and O, originated in Southern China and by 10,000 years ago went on to populate first Southeast Asia and then from Southeast Asia, left for East Asia. Roughly 12,000 years ago, during the Neolithic period, farmers settled along the Yellow River. Alongside various other lineages including O2‐M122, they initiated the development of agriculture.. About 6000 years ago, ancestors of the Tibetans split off from this parent group. About 5,000 years ago, Neolithic Yellow River farmers experienced rapid expansion, with notable gene flow into surrounding populations.
This corresponds to the late period (2600-2000 BC) of the Longshan culture in the middle Yellow River area. As the Neolithic population in China reached its peak, the number of settlements increased. In some locations, such as the basin of the Fen River in southern Shanxi, the Yellow River in western Henan (confined by the Zhongtiao Mountains and Xiao Mountains), and the coastal Rizhao plain of southeast Shandong, a few very large (over 200 ha) centers developed. In more open areas, such as the rest of Shandong, the Central Plain (in Henan) and the Wei River basin in Shaanxi, local centers were more numerous, smaller (generally 20 to 60 ha) and fairly evenly spaced. Walls of rammed earth have been found in 20 towns in Shandong, nine in the Central Plain, and one (Taosi) in southern Shanxi, suggesting conflict between polities in these areas.
 The expansion and rise of these various settlements could be due to the impetus of the collective benefit of the construction of irrigation works in the late Neolithic:
 "Most of the labor to dike and drain an area is associated with digging a ditch and sidecasting the soil to make an earthen dike. To make the culvert and tide gate you can use an old worn-out canoe for the pipe .... and use just about any good-sized flat stones you can get your hands on. If you have twice as many people making your dike, you can make twice as many linear feet of dike. Doubling the perimeter of a square dike results in quadrupling the area within the dike."
 The agricultural surplus would have allowed for a rapidly expanding population, which would provide more labor for irrigation. By the time of the establishment of the Xia and Shang dynasties, population estimates were at approximately 13 million people.
 Studies of DNA remnants from the Central Plains area of China 3000 years ago show close affinity between that population and those of Northern Han today in both the Y-DNA and mtDNA. Both northern and southern Han show similar Y-DNA genetic structure.
 Y-chromosome haplogroup O2-M122 is a common DNA marker in Han Chinese, as it appeared in China in prehistoric times. It is found in more than 50% of Chinese males, with frequencies tending to be high toward the east of the country (30/101 = 29.7% Guangxi Pinghua Han, 13/40 = 32.5% Guangdong Han, 11/30 = 36.7% Lanzhou Han, 26/60 = 43.3% Yunnan Han, 251/565 = 44.4% Zhaotong Han, 15/32 = 46.9% Yili Han, 23/49 = 46.9% Lanzhou Han, 32/65 = 49.2% South China Han, 18/35 = 51.4% Meixian Han, 22/42 = 52.4% Northern Han, 43/82 = 52.4% Northern Han, 18/34 = 52.9% Chengdu Han, 154/280 = 55.0% Southern Han, 27/49 = 55.1% Northern Han, 73/129 = 56.6% North China Han, 49/84 = 58.3% Taiwan Han, 35/60 = 58.3% Taiwan Minnan, 99/167 = 59.3% East China Han, 33/55 = 60.0% Fujian Han, 157/258 = 60.9% Taiwan Han, 13/21 = 61.9% Taiwan Han, 189/305 = 62.0% Zibo Han, 23/35 = 65.7% Harbin Han, 29/44 = 65.9% Northern Han, 23/34 = 67.6% Taiwan Hakka, 35/51 = 68.6% Beijing Han).
 Han Chinese are genetically distinguishable from Yamato Japanese and Koreans, and internally the different Han Chinese subgroups are genetically closer to each other than any of them are to Koreans and Japanese. Howerver, some Southern Han chinese, such as Guangxi Han, are genetically closer to Vietnamese and Dai people than Northern Han. But meanwhile when compared to Europeans genetics, the Han Chinese, Southeast Asian, Japanese and Koreans are closer to each other than Europeans and South Asian. Genealogical research has indicated extremely similar genetic profiles of a less than 1% total variation in spectrum between these three groups. Some Southern Han Chinese and Northern Han Chinese are closest to each other and show the smallest differences when they are compared to other Asians. Vietnamese Ho Chi Minh City Kinh are close to Xishuangbanna's Dai ethnic minority and Guangdong Han Chinese. Koreans are also relatively close to northern Han Chinese. Japanese are more genetically distant from Koreans than Koreans are from northern Han Chinese. However Buryat Mongols and Qinghai Mongols are further from each other than Japanese and Korean despite both being Mongols. Comparisons between the Y chromosome SNP and MtDNA of modern Northern Han Chinese and 3,000 year old Hengbei ancient samples from China's Central Plains show they are extremely similar to each other and show continuity between ancient Chinese of Hengbei and current Northern Han Chinese while Southern Han Chinese were different from the people of Hengbei. This showed that already 3,000 years ago the current northern Han Chinese genetic structure was already formed.
 The mitochondrial-DNA haplogroups of the Han Chinese can be classified into the northern East Asian-dominating haplogroups, including A, C, D, G, M8, M9, and Z, and the southern East Asian-dominating haplogroups, including B, F, M7, N*, and R.
 These haplogroups account for 52.7% and 33.85% of those in the Northern Han, respectively. 
 Haplogroup mtDNA D descend from Dravidian Haplogroup M mtdna is the modal mtDNA haplogroup among northern East Asians. Among these haplogroups, D, B, F, and A were predominant in the Northern Han, with frequencies of 25.77%, 11.54%, 11.54%, and 8.08%, respectively.
 However, in the Southern Han, the northern and southern East Asian-dominating mtDNA haplogroups accounted for 35.62% and 51.91%, respectively. The frequencies of haplogroups D, B, F, and A reached 15.68%, 20.85%, 16.29%, and 5.63%, respectively.
 During the Last Glacial Maximum, 29,000 to 18,000 years ago, northern China was a treeless steppe with areas of permafrost and southern China lost much of its forest cover. The sea level was much lower. Borneo, Indonesia, the Philippines, and the Japanese archipelago may have been accessible by land. With the end of the last ice age, a period of warming occurred lasting from 18,000 to 10,000 years ago. The oceans rose and inundated vast regions leaving little trace of coastal settlements used by these people. We know little about their languages. Their cultures are likely to have been diverse. There are many limestone cave sites in southern China which show human settlements. There is evidence of pottery making. The inhabitants had bone tools, fished, and hunted pigs and deer.
 It is believed that the climate in southern China was warmer and wetter south of the Qing Ling mountains; elephants are known to have inhabited the Yangtze river region. The climate in Northeast China north of present-day Beijing was characterized as a cold steppe environment during this period. The presence of woolly mammoth is well documented.
 The climate was also much warmer between 8,000 and 3,500 years ago. In the Shandong region, excavations have found the bones of alligators and elephants.
 The development of agriculture about 10,000 years ago, with the domestication of millet in the Yellow River valley region and rice in the Yangtze River valley, may have been associated with accelerated growth in the number and size of settlements and the intensified development of local cultures and languages.
 Early settlements in the Chinese Upper Paleolithic were either hunter-gatherer societies, or marine environment based societies characterized by shell middens. Relatively speaking the land was sparsely populated, as the peoples followed the coastal regions and the river valleys.
 Neolithic settlements have been found from Liaoning province in the northeast to the Chengdu region in the southwest; from Gansu province in the northwest to sites in Fujian in the southeast. The settlement pattern in the Tibetan region is still unclear as there is debate as to whether there was a pre-Neolithic population movement into the region.
 The origin of Sino-Tibetan is uncertain. It dates to the Neolithic, or just before the Neolithic. There are various proposals.  Van Driem (2005) proposes that Sino-Tibetan originated in the Sichuan Basin before 7000 BC, with an early migration into northeast India, and a later migration north of the predecessors of Chinese and Tibetic.[citation needed] Matisoff (1991) places its origins in the eastern part of the Tibetan plateau around 4000 BC, with the various groups migrating out along the Yellow, Yangtze, Mekong, Salween and Brahmaputra rivers.[citation needed] Blench and Post (2014) have proposed that the Sino-Tibetan homeland was in northeast India, the area of greatest diversity, around 7000 BC.[citation needed] Blench (2009) proposes that the earliest speakers of Sino-Tibetan were not farmers, since agriculture cannot be reconstructed for Proto-Sino-Tibetan. Rather, early Sino-Tibetan speakers were highly diverse hunter-gatherers and foragers.  More recent study published in the Proceedings of the National Academy of Sciences of the United States of America point to the origin of the Sino-Tibetan in northern China in the Neolithic Cishan culture and Yangshao culture.
 The Austroasiatic languages (including Vietnamese, Khmer, etc.) likely originated from Southern China and would have entered Southeast Asia via Yunnan and the Mekong. Likewise, the Miao, Thai, Burmese, and Tibetan languages evolved in China. It is even accepted that proto-Austronesian speakers originated from China, migrated to Taiwan (Formosa), and then to the islands of the Pacific, especially since Taiwan is the place exhibiting the most diversity in Austronesian languages (see Formosan languages). By 3,000 years ago, the sophistication of some of the cultures neighboring that of the Han Chinese can be seen in the bronze artifacts of the Sanxingdui (Sichuan), Ban Chiang (Thailand) and Dong Son (Vietnam). The domestication of the horse 6,000 years ago in the Eurasian steppes led to cultures that mixed animal husbandry and agriculture. Indo-European speakers are known to have reached the Xinjiang region 4,000 years ago (see Tocharians).
 Because the East Asian landmass was initially populated from the south, and the historical record shows the Han Chinese migrating to the south and southwest, the genetic relationship among all the peoples of China remains a challenging study.