There was actually not much time difference between Japanese settlement in northern Hokkaido and that in southern Sakhalin.

Though the Andō clan settled the south end of the Oshima peninsula in the 15th century, it was not until 17th century that Japanese authority arguably extended to the northern tip of Hokkaido. In 1604, the Matsumae domain was granted the right to monopolize trade with the Ainu by the shogunate, and established akinaiba or basho (trading offices) all along the coasts of Hokkaido, including Teshio basho in Keichō era (1596-1615). During Shakushain’s revolt in 1669, there was an Ainu uprising in Mashike, but was soon put down.

In 1685, the domain opened Sōya basho at the northernmost point of Hokkaido, which administrated cross-strait trade with Karafuto Ainu. In 1752, Katō Kahei, an official at Sōya basho, opened fishery offices at Kushunkotan (Korsakov) and two other locations in Sakhalin. For following decades, the domain and the shogunate sent several expeditions to Sakhalin, but by this time, Russians were already active near Japanese settlements. In 1804, Nikolai Rezanov finally arrived at Nagasaki to discuss the border, but was rejected, and his man Khvostov attacked Kushunkotan in 1806.

It is clear why Japanese settlement in Hokkaido was so late and slow. It was too cold to grow rice. In feudal Japan, the whole point of acquiring land was to collect tax in rice. In this regard, land in Hokkaido (and Sakhalin) was literally of no value, or zero koku by the measurement introduced in 1580s.

This was also why the Matsumae domain was granted a commercial right, instead of land in fief like other daimyo. Surely they made profits from trade with the Ainu, fishery and placer mining, but they were not enough to sustain their development in such severe natural environment, which entirely depended on import from Honshu for rice and other products. Eventually, Hokkaido was put under the direct control of the shogunate in 1807, who had seen the domain’s inability to manage the island.