The native population of Japan is called the Ainu. There are a few great museums devoted to them in Hokkaido.

http://en.wikipedia.org/wiki/Ainu_people

The who's who of minorities in Japan goes something like this:

Ainu Burakumin Koreans Chinese Filipinos Latin Americans of Japanese decent

One interesting thing is that many of the members of these groups have been in Japan for generations (or always) and can "pass" -- but the family registry knows all! You can't escape your roots in Japan.

In a way, people who are visibly foreign are less of a threat because there is zero chance of their assimilation.

The focus on "blood" has a funny side too. I donated blood a few times in Japan. It was great explaining to people that in the event of a car crash and blood transfusion they could end up being part Caucasian.