Rotem Kowner has an interesting article in Ethnohistory, Skin as a Metaphor (Project Muse subscription required), that deals with European perception of the Japanese during the period in which Japan was isolated. The evolution of perception was due completely to the changes in scientific discourse in Europe, which increasingly obsessed on skin color. Although they did not escape becoming an inferior race, the Japanese were not described with the same harsh language as other non-Europeans.

[Linnaeus‘] followers maintained his focus on color as a major component of their racial classification: The Scottish anatomist John Hunter (1728–1793) depicted Mongoloids as brown, whereas Johann Blumenbach was apparently the first to depict the peoples of East Asia as yellow. This color better suited the Japanese, for whom the designation brown was frequently far from reality. The Europeans could easily see yellow in others’ skin color because it is so vague, and it was enough that a few members of a group were perceived as such to generalize the characteristic to the whole group.

In 1775, the year Blumenbach’s book was published, the Swedish botanist and Linne’s disciple Charles Peter Thunberg (1743–1828) left for Japan. Thunberg, who worked as a physician at the Dutch mission for one year, was the first naturalist of the new school to examine the Japanese. A decade later, when Thunberg wrote his own account of his experience in Japan, he depicted the Japanese as having “yellowish colour over all, sometimes bordering on brown, and sometimes on white.”