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How did Shinto (the traditional Japanese polytheistic religion) explain human origin?

Also, does it have a flood myth?

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The Yamata no Orochi (八岐大蛇) is actually ‘the flood myth’ of Japan. The 8 heads of Orochi are actually 8 rivers. Can’t remember the source, will update again if possible.

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The Kojiki of Shinto states the origins of mankind as an action of Izanami-no-Mikoto:

Izanami started his cleansing rites and in doing so he created the Goddess of the seas and the Goddess of the moon by washing his left and right eyes. He then created the God of storms out of his nostril and after all this was done he created the first humans.

I should probably also point out that the term "polytheism" as it is understood in the West doesn't really apply to Shinto. The term "kami" describes a spirit or essence that is very much part of the world. Naturalistic animism would probably be a better description.

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