Emishi become Ainu or Japanese in the Medieval period

The Emishi were unlike modern Japanese. One line of thinking in Japanese society is to assume that the Emishi were like today’s Japanese because the Ainu does not possess power or influence.  This anachronism (or reading the present into the past) has to do with prejudice towards their descendants, the Ainu. This becomes clear when we look at the way their descendants are perceived in modern Japanese society as a people who are not relevant. The underlying assumption is: how could their ancestors have been so effective against the Japanese forces? How could they have fundamentally altered the battle tactics of the Japanese army? They therefore could not have been related to the Ainu.
The Ainu are a peaceful people so how could their ancestors have fought so effectively? They lived by hunting and gathering so how could they have fielded armies, let alone effective ones? Much of the interpretation is based on the exploited Ainu of the nineteenth century who were subservient to the Japanese.  For one thing none of these assumptions are true of their history.
The Ainu during historical times were not always peaceful nor were they ineffective. During much of the medieval and early modern periods they held their own against numerous enemies effectively. They successfully fought the Japanese to a standstill for centuries, keeping them out of much of Ezo-ga-shima (Hokkaido). They successfully fought off the Mongols during the height of their imperial expansionist phase in the thirteenth century. They even carved out a trading sphere of influence of their own in the early modern period that saw their armies fight in the Amur river valley against Ming forces in the seventeenth century.
There is a dark side to this as well which preceded the rise of the Satsumon culture in Hokkaido and the Hiraizumi in the Tohoku. The dismembered remains of skeletons found in archaeological digs recently unearthed from Aomori prefecture thought to be from the tenth century in areas that were under independent Emishi indicates they fought fiercely against each other for control of the remaining lands and access to trade with the Japanese state. This age of internecine conflict over trade between the end of the Conquest in 811 ushered in a time period of about two centuries during which the Emishi fought one another. The Hiraizumi rulers united the area under their control effectively ending this fighting in the eleventh century. 
This was the defining moment when the Emishi split into two groups: the Hokkaido Emishi split off from the Tohoku Emishi as the two groups fought against each other during this time of conflict.  So even though the Tohoku Emishi whose main groups the Tsugaru Emishi and the oku-chi Emishi fought each other over the trade between the Hokkaido Emishi and Japan they often united as fushu (allies) of the Japanese when it came to fighting off their common enemy their Hokkaido brethren.  The Hokkaido Emishi were powerful enough during the ninth century that they continually threatened the Japanese outposts in the Tohoku, and earned the enmity of the remaining Emishi of the Tohoku who saw them as a common enemy in the trade with Japan.           
Those Emishi who stayed in their traditional Tohoku lands became more like other Japanese as time went on both ethnically and culturally as they became fushu.  Those Emishi who moved further north to Ezo-ga-shima created the Satsumon culture, and became further separated from the Tohoku Emishi. However, during the transition which lasted a few hundred years after the Emishi conquest, trade and movement of people took place across the Tsugaru strait between northern Honshu and Hokkaido.  It can be concluded that as they moved further north the Emishi continued to not just retain their Jomon/epi-Jomon ethnicity but actually strengthened them, and became further unlike those who lived under Japanese rule. There was still a largely unchanged Jomon population living in Hokkaido, so those Emishi who separated from the Tohoku and began living in Hokkaido became within a few generations much more Jomon in appearance. 
What happened to the Emishi who lived in Hokkaido is that they became ethnically isolated because they did not allow Japanese settlement into their territory after the medieval period.  Also, rice cultivation though practiced was not done exclusively, so their economy was still partly based on hunting and gathering. Up till the Shakshain War of the mid-seventeenth century they were able to maintain a powerful state that controlled the trade between Japan and the Amur river valley. Interestingly, as a peaceful trade took place between the Ezo of Hokkaido and the Asian Amur peoples such as the Gold, Olchagold and Gilyak peoples there was some ethnic intermixing. The extent is unknown, however, some Ainu types in the nineteenth century were of Amur extraction, East Asian in appearance, but not Japanese. This is likely related to the little known history of their incursions into the Amur river valley during the early seventeenth century to further their control over the san-tan trade as middlemen between Japan and the Amur valley. 
Ironically, a fushu family the Ando (and from them the Kakizaki), became middlemen in the trade between the Ainu of Ezo-ga-shima (Hokkaido) and Japan. This family started out as fushu in the Kamakura period and built up their power in Akita before they extended their power towards Ezo-ga-shima. However, the Ainu were very powerful during the medieval period so the Ando and Kakizaki families did not make significant inroads into Hokkaido. They were able to consolidate their power as Emishi kanrei (alternate reading, Ezo kanrei) a title they received from the Kamakura Shogunate, over other competing families in northern Tohoku.
The Ando family is variously described as originating as a local family on the Tosa-minato, the Tsugaru area, or as direct descendants of the Abe family of the eleventh century.  Most sources treat them as actual aboriginal Emishi who had become Japanese.  Again, as with the Abe it is hard to separate fact from conjecture. If they are descendants of the Abe they are most likely of Japanese descent, however, they became prominent after the Kamakura period in an area still dominated by half Emishi and Japanese of Watarito (Tsugaru), so at the very least their existence is dependent on their status as a frontier warrior family which they retained when they moved to Hokkaido.
This is where this story ends. It begins with the Emishi people living on the main island of Japan. It ends fittingly with the last identifiable descendants of the Emishi becoming part of the Japanese warrior class, and their complete cultural conversion. They then carry on the mission that the Japanese themselves started centuries ago by trying to subjugate the Ainu, themselves split off from the Honshu Emishi a millennium ago.
In modern Japan Emishi live on in such movies as Miyazaki’s Mononoke hime. At least he portrayed these people accurately as Jomon people. Just as in the movie they were outside the state, wary of the Japanese. They detested the Yamato state and their efforts to limit their freedom just as much as Native Americans detested the Europeans. They fought for their freedom, their way of life for centuries against their more numerous foes, and in the end they lost their way of life, having to adapt themselves to their conqueror's ways. The only mitigating factor was that the terms of their incorporation into the state was far less onerous in the ninth and tenth centuries than those who were incorporated in Hokkaido in the eighteenth and nineteenth centuries.
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Kenjiro 2006.3.1 (revised 2015.12.17)