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If the two numbers are an ISBN-10 and an ISBN-13, then it does not matter. They are just two different identifiers for the same book, and if you look closely, you'll see that digits 4 through 12 of the ISBN-13 are the same as digits 1 through 9 of the ISBN-10.
If you see two ISBNs that are the same length, then most likely one is for a paperback and one for a hardcover. You must use the one that brings up the correct binding type for the book you have.