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Oyumino district (Chiba City, Chiba Prefecture, Japan) is a small residential area which has been intensely investigated as part of an urban development project during the 1970s~90s. The emergency excavations have yielded a vast amount of archaeological materials from different historic and prehistoric periods, including numerous hunter-gatherer settlements attributed to the Jōmon culture (ca. 16,000 – 2500 cal BP). The dataset comprises the spatial location of 364 residential units attributed to the Middle and Late Jōmon periods (ca. 5500-3200 cal BP) along with the spatial extent of the excavation areas, the 5-meter resolution digital elevation model of the Oyumino district, and an attribute table which includes the probability of existence of each pithouse for chronological intervals of 100 years.