Nobody knows where Hobbits come from. Tolkien deliberately left them a mystery to us as well as the other people of Middle-earth to facilitate Frodo's not being known about/discovered by Sauron. They were not mentioned at all in the Silmariliion, for that reason. No one, including themselves, knows where they came from.
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"Man as a whole, Man pitted against the universe, have we seen him at all 'til we see that he is like a hero in a fairy tale?"
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