There is a theory of a link with asian aborigenes (not australian ones) for both the Ainu and the Jomon people that were there before the Ainu, based on the bone structure. The Ainu came from Sakhalin to the archipelago towards the end of the Jomon era. The Ainu and the Jomon may possibly be from the same genetic group or similar genetic groups, but they were very distinct cultures. The Jomon culture ran from about 10500 BCE to about 300 BCE.
Genetic analysis does point to a North-eastern Asian ancestry for both the Jomon and Ainu people. It's far from settled tho