Sites have been discovered from southern Kyushu to northern Hokkaido, but most are small and only stone tools have been preserved due to the high acidity of the Japanese soil.

As the Paleolithic peoples probably occupied the wide coastal shelves exposed by lower sea levels during the Pleistocene, the majority of sites are most likely inundated.

[1] The study of the Japanese Paleolithic period is characterized by a high level of stratigraphic information due to the volcanic nature of the archipelago: large eruptions tend to cover the islands with levels of Volcanic ash, which are easily datable and can be found throughout the country as a reference.

[5] One of the most important sites dating to these times is Lake Nojiri, which dates to 37,900 years Before Present (~36,000 BC), which shows evidence of butchery of two of the largest extinct megafauna species native to Japan, the elephant Palaeoloxodon naumanni, and the giant deer Sinomegaceros yabei.

Japanese Paleolithic tool implements thus display Mesolithic and Neolithic traits as early as 30,000 BC.

[10][11] During much of this period, Japan was connected to the Asian continent by land bridges due to lower sea levels.

[16][17] One study, published in the Cambridge University Press in 2020, suggests that the Jōmon people were rather heterogeneous, and that many Jōmon groups were descended from an ancient "Altaic-like" population (close to modern Tungusic-speakers, represented by Oroqen), which established itself over the local hunter gatherers.

This “Altaic-like” population migrated from Northeast Asia in about 6,000 BC, and coexisted with other unrelated tribes and or intermixed with them, before being replaced by the later Yayoi people.