What is the difference between もと ( 本) and もと (元)
In my textbook they are both presented as meaning "origin".

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Oh, I see. I will focus on learning the Kanji combinations then. Thank you very much!

Answer

There are very slight difference between them.
Even in Japan, very few people know the difference.

Originally,
「本」is used to represent something which is related to basis or essence.
¨「元」 is used to represent something which is related to origin, cause, root, or money resource.
But every phrase with these kanji does not always follow this rule.

I recommend you to just learn some words which uses these kanji.

例
資本（shihon)　capital, fund

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