The most frequent type of residential structure at Sannai Maruyama is a pit dwelling. Like the thatched tipi form, the floor of a pit dwelling was dug into the ground. Then, supporting posts were placed at the corners and the walls and roof were built and roofed with thatch. The average size of a pit dwelling is between three and four meters in diameter with a 12 square meter floor plan.
The earliest pit dwellings at Sannai Maruyama were during the Early Jomon period, built between 5900 and 5400 years ago. At that time, Sannai was comparatively small and simple, a collection of pit dwellings and the beginnings of a midden (refuse dump).