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There are two probable reasons:
1. Most Kindle books are created using Amazon's "Kindlegen" tool. This includes a copy of the complete HTML source into the book, which increases the size considerably.
2. ePub files use a much more efficient compression method than Mobipocket format does.
As Paul notes, if the book is illustrated it's possible that the Kindle version has higher-resolution images than the ePub version does.
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