The war developed into a last try by the Ainu to keep their political independence and regain control over the terms of their trade relations with the Yamato people.

According to scholar Brett Walker:[1] The war of Shakushain stands out as a watershed event in the history of the conquest of Ezo.

Shakushain exploded onto the scene as a charismatic leader who proved able to bridge regional differences among Ainu communities, threatening to unite them against the Japanese intrusion from the south.

The Tokugawa shogunate reacted by solidifying its own united front of military allies in the northeast, replacing local Matsumae generals with men of its own choosing, thus illustrating its self-appointed role as defender of the realm.

Those unable to support themselves had no choice but to work as forced labor in fish factories in Honshu on a salary about a seventh of the rate paid to the Yamato.