For a long time Sakhalin and the Kurile Islands were, archaeologically speaking, "Terra Incognita", though since the end of the 19th century Russian and foreign explorers had pondered the prehistory of the islands. Now, as a result of the researches of Russian and Japanese archaeologists, about a thousand archaeological sites are known in the Sakhalin region. They date to various cultural eras from the palaeolithic to the modem. Each year Sakhalin archaeologists carry out excavations in nearly all districts of the region. There are about 60,000 finds in the museum, from about 250 archaeological sites. International archaeological and ethnographic expeditions with American and Japanese scientists have been organised since 1990.

One of the main tasks of Sakhalin archaeology is to study the earliest palaeolithic settlements on Sakhalin and the Kurile Islands. The collection has pre-historic choppers and flake tools from palaeolithic sites on Sakhalin and the Northern Kurile Islands, some as old as 25-30,000 years. A group of obsidian blade tools from the Upper Palaeolithic sites of Sokol and Takoye II in southern Sakhalin date from 18-11,000 years ago. Photos of excavations and finds from the Imchin and Sadovniki sites describe neolithic remains dating from 5000-1000 years ago. All these artifacts demonstrate distinctive island cultures, but also prove close connections and mutual influences between the ancient inhabitants of Sakhalin and the Kuriles, and the peoples of nearby Japan and the Primorye region of Russia. Stone and bone articles and ceramic vessels give an idea of the Okhotsk culture of South Sakhalin and the Kurile Islands, about 2000 years ago. It was based on sea fishing, hunting, and coastal gathering.

The artifacts of the Ainu culture, a people indigenous to Sakhalin and the Kuriles, are unique. The remains of Ainu dwellings and burials attract special attention, and the collection includes typical Ainu tableware -ceramic flat-bottomed vessels with small inner ears - and from Ainu burials, a set of funeral goods dated to the 16-17th century. The Ainu material culture shown here, along with some archaeological finds, is borne out by ethnographic evidence from the 19th century.