Much like the Native American who is represented by a large number of different tribes, so the Emishi were also represented by different tribes with different ways of life. The Emishi were semi-nomadic and relied on their horses in warfare.
The first major attempts to finally subjugate the Emishi by the emperors of Japan, particularly Emperor Kammu in the late 8th century were largely unsuccessful. The imperial armies modelled after the mainland Chinese were no match for the guerilla tactics of the Emishi.
As during the 9th century the emperors began to rely on the powerful regional clans - introducing the title of Shogun and the basis of the Samurai - and with the development of horse archery the Emishi were driven to Hokkaido. By the mid 9th century their land in Honshu was conquered.
Soon after the Second World War mummmies were discovered in Hiraizumi (the capital city of the Northern Fujiwara) who were thought to be related to the Emishi who had originally submitted to Yamato rule, and hence were thought to have been related to the Ainu. However, after further research on the mummies it was found that the rulers of Hiraizumi were like other Japanese of the time, and certainly not related to ethnic Ainu. This was seen as evidence that the Emishi were not related to the Ainu. This had the effect of popularizing the idea that the Emishi were like other contemporary ethnic Japanese who lived in northeast Japan, outside of Yamato rule.
This viewpoint went hand in hand with the idea that the Japanese were a single ethnic group that had undergone little change since antiquity. Nothing could be further from the truth.
Japan was a melting pot of many different ethnic groups ranging from continental Asians, both distant in time, such as those related to Native Americans, and more recent migrants such as the Chinese and Koreans, as well as various groups of Pacific Islanders related to the Polynesians. In the study of Jomon skeletal remains dating from thousands of years ago, a very ancient Asian was recovered, someone who was directly ancestral to the Ainu. This said, it was found that diachronically, and geographically, the skeletal structure of the Jomon population changed over time from southwest to northeast, paralleling the actual migration of Japanese speakers historically.
Even relying on historical documents, it was clear that the ancestors of the Ainu left many Ainu place names in the main island of Honshu, indicating that an Ainoid population had lived in the area before the Yamato expansion. Further, even as late as the nineteenth century, there were remnant Ainu who were living in Aomori province in far northeastern Honshu. Though still inconclusive, the main body of Satsumon culture, seen by all scholars as definitely ancestral to Ainu culture in Hokkaido, may have gotten its start from migrants from northeastern Japan.
Finally, the so-called Emishi rulers of Hiraizumi were not actually direct descendants of that ethnic group and therefore cannot be seen as any sort of evidence. It was customary for local rulers to take on local titles that would suggest a direct ancestry. There is no doubt that the Northern Fujiwara had some Emishi blood in them a few generations removed, but for the most part they were from the Japanese aristocracy. For example, many Ainu in Hokkaido today, are typically one-fourth to one-eighth Ainu, and cannot be easily distinguished from other ethnic Japanese. Even though the pattern of assimilation is not known in detail for the Emishi who fought against Yamato (Japanese) control in northeast Honshu, ethnic characteristics are lost after three generations of intermarriage or interbreeding in areas that did not remain isolated from the immigrant Japanese population that poured into the area after the conquest.
In a time when the Ainu of Hakkaido have been more vocal in breaking the majority's silence in regard to the ethnic diversity of Japan, their history is still being denied them through the back door--a history that was not just confined to Hokkaido but included the rich cultural heritage of the main island of Honshu.