Two main perspectives on culture and ethnic identity will be covered: one, has to do with similar ethnic groups with different cultures; the other has to do with different ethnic groups with similar cultures. The two issues are quite different from each other, and point to different conclusions. However, it needs to be addressed in order to clarify what the different groups such as Emishi/Ezo and Ainu are and how they differ from the Japanese. This is a vital discussion particularly for the twenty-first century.
Even if the Emishi were ethnically similar to other Kanto people under Yamato rule they still had a different culture from the Yamato Japanese. We know now that the Emishi were different from the Kanto groups ethnically, being closer to the later Ainu, however, we also know that some ancient Japanese frontier clans sided with the Emishi in their battles against the Yamato. These frontier families, some of whom became influential members of Emishi society, were ethnically similar to other contemporary Japanese (from the Kanto), but were different culturally from them. These frontier clans most likely were a kofun type population, so they were mid-way between Jomon/Ainu and Yayoi, so if they sided with the Emishi and adopted their lifestyle it would have been somewhat difficult to tell them apart from their Emishi neighbors.
The contrast between Emishi and ancient Japanese was not as great as that between the later Japanese and the Ainu both in terms of external appearance and culture. Externally, the ancient Japanese settlers were ethnically closer to the Jomon, and their hairstyle was not too different from the Emishi--they allowed the growing of beards. It was not until the Tokugawa period when the topknot and shaved head became the norm among Japanese. Culturally too, the kofun culture had influenced the Emishi in both their burial practices and their military equipment though the language spoken was different as was their lifestyle.
Similarly, there were Japanese who sided with the Ainu in their conflict with the Matsumae during the Shakshain War of the seventeenth century. These Japanese though similar ethnically to other Japanese would appear like other Ainu due to the contrasting cultural styles. For example, the "Japanese Ainu" would have worn their hair long and unshaven. They would also have allowed their beards to grow untrimmed. The Japanese who were part of the Matsumae would not recognize these others as Japanese as they themselves had samurai-style haircuts with a top knot and clean shaven forehead. The greatest irony of this whole war is that most of the Japanese participants in this conflict were themselves from the northern Tohoku region. Those Japanese who opposed the Matsumae were able to grow beards and became themselves participants in Ainu culture to the point that the Matsumae themselves considered them to be Ainu. Many were distantly related to the Emishi which allowed them to "fit in."
The cultural differences and rule against "crossing over" was rather draconian. In order to preserve their trade monopoly with the Ainu in Hokkaido, the Matsumae forbade them from wearing their hair like the Japanese, and Japanese subjects were not allowed to grow a beard or to grow their hair like the Ainu. This resulted in strange behavior where Ainu influenced by Japanese culture would appear as other "Japanese" in their hair style until the uimam had to be performed. The uimam was a formal, ceremonial meeting between the Matsumae and the Ainu chiefs. During these formal meetings the Ainu were required to "look Ainu." So some Ainu who had adopted Japanese culture purposely grew their hair and beards back just for this meeting alone. Despite how much modern Ainu condemn the Matsumae in limiting Ainu choices it can be argued that, ironically, if it were not for the Matsumae many of the traditions of the Ainu would not have been preserved. Left alone the Ainu culture would have eventually become very tenuous in the face of Japanese settlement and conquest. Japanese settlement was severely limited by the Matsumae to preserve their only lucrative source of income--trade with the Ainu. Even with this restriction Japanese merchants did settle among the Ainu to try and break this monopoly--these are the ones who sided with Shakshain in his war against the Matsumae.
Then there are real ethnic or racial differences that would not have allowed an easy cross over from one group to another. The mainly Yayoi Japanese from western Japan (including most Japanese today) would have had a hard time "passing" as an Emishi or Ainu due to not being able to grow a beard or having dissimilar features. However, it was not just outward appearance, but other cultural markers such as lifestyle, ritual and religion that made one Japanese or Emishi on the one hand or Japanese and Ainu on the other, particularly where these groups met on the frontier. For example, on Sakhalin island north of Hokkaido, the people there contrasted ethnically from the Hokkaido Ainu, but had a culture that was virtually identical to them. The Sakhalin Ainu were ethnically related to the Amur river peoples, not to the Hokkaido Ainu, but they practiced the same ceremonies and lived by hunting and gathering.
In the modern period there are many Ainu and half Ainu who live like other Japanese, sharing the culture and speaking the language. But just because they share the culture does not mean they are Japanese, or that they define themselves in the same way culturally. This is hard for most Japanese to understand. In a similar way, most mixed Emishi descendants, known today as Tohoku-jin (Tohoku people) are completely assimilated into Japanese culture, but the way they define their relationship to other Japanese, and the way they see themselves differs from the way other Japanese living elsewhere see them.
Recently, in Iwate prefecture, they have put up memorials to Aterui and Moro so perhaps in that area there are those who would directly identify themselves as Emishi than in other areas of the Tohoku whether this is based on a real relationship or not. This would make sense since that prefecture formed the heart of the ancient land of Hitakami.
How an entire nation and people, the Emishi, were conquered and in some cases absorbed, and in other cases destroyed by the Japanese state will hopefully influence the future of the Japanese themselves by bringing about racial and cultural acceptance, because this history is not about one unique ethnic or racial group living in harmony and consensus, but more about how a mix of cultures and ethnic groups were eventually united through conquest and assimilation. Though this maybe ancient history it is the ideology of Empire that first justified the conquest of the Emishi nation of Hitakami. This ideology is still around, but has been dealt a serious setback after the last century.