Fossils found in Kenya have shown that primates inhabited the area for more than 20 million years. Recent findings near Lake Turkana indicate that hominids such as Homo habilis (1.8 to 2.5 million years ago) and Homo erectus (1.9 million to 350,000 years ago) are possible direct ancestors of modern Homo sapiens, and lived in Kenya in the Pleistocene epoch.

During excavations at Lake Turkana in 1984, paleoanthropologist Richard Leakey, assisted by Kamoya Kimeu, discovered the Turkana Boy, a 1.6-million-year-old Homo erectus fossil. Previous research on early hominids is particularly identified with Mary Leakey and Louis Leakey, who were responsible for the preliminary archaeological research at Olorgesailie and Hyrax Hill. Later work at the former site was undertaken by Glynn Isaac.

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East Africa, including Kenya, is one of the earliest regions where modern humans (Homo sapiens) are believed to have lived. Evidence was found in 2018, dating to about 320,000 years ago, at the Kenyan site of Olorgesailie, of the early emergence of modern behaviours including long-distance trade networks (involving goods such as obsidian), the use of pigments, and the possible making of projectile points. It is observed by the authors of three 2018 studies on the site, that the evidence of these behaviours is approximately contemporary to the earliest known Homo sapiens fossil remains (such as at Jebel Irhoud in Morocco and Florisbad in South Africa), and they suggest that complex and modern behaviours had already begun in Africa around the time of the emergence of the species Homo sapiens. Neolithic

The first inhabitants of present-day Kenya were hunter-gatherer groups, akin to the modern Khoisan speakers.These people were later largely replaced by agropastoralist Cushitic (ancestral to Kenya's Cushitic speakers) from the Horn of Africa. During the early Holocene, the regional climate shifted from dry to wetter conditions, providing an opportunity for the development of cultural traditions such as agriculture and herding, in a more favourable environment.

Around 500 BC, Nilotic-speaking pastoralists (ancestral to Kenya's Nilotic speakers) started migrating from present-day southern Sudan into Kenya.Nilotic groups in Kenya include the Kalenjin, Samburu, Luo, Turkana, and Maasai.

By the first millennium AD, Bantu-speaking farmers had moved into the region, initially along the coast. The Bantus originated in West Africa along the Benue River in what is now eastern Nigeria and western Cameroon.The Bantu migration brought new developments in agriculture and ironworking to the regionBantu groups in Kenya include the Kikuyu, Luhya, Kamba, Kisii, Meru, Kuria, Aembu, Ambeere, Wadawida-Watuweta, Wapokomo, and Mijikenda, among others.

Notable prehistoric sites in the interior of Kenya include the (possibly archaeoastronomical) site Namoratunga on the west side of Lake Turkana and the walled settlement of Thimlich Ohinga in Migori County.

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